Update. After almost a week of messing with it, I got everything working. BLUF: the only thing that has made sense is that there is a problem with my Raspberri Pi.

I started by using bossa and reflashing the duet 3... that didn't fix the problem.
I remembered I had a few Raspberri Pi 3 laying around from other projects as well as I had purchased another duet 3 for my other printer. I decided to swap out one thing at a time, starting with a new SD card.
I then used the new SD card and started with a fresh Duet Pi image. I was still getting errors/incompatble firmware and Error: M997: Failed to find IAP file /opt/dsf/sd/sys/Duet3_SBCiap_MB6HC.bin
I went back to follow the https://duet3d.dozuki.com/Wiki/Getting_Started_With_Duet_3#Section_Updating_Duet_3_from_RRF3_0_Beta_12_to_3_0_Final_via_DWC
After following that Wiki, it got rid of the incompaable firmware but still said it was missing the Duet3_SBCiap_MB6HC.bin

I then changed only the Raspberri Pi keeping the same SD card and Duet, and after the sudo updates/upgrades everything was working.

After that I was done with that duet 3 and SBC setup I decided to setup my other new duet 3 and duplicate what I did as both setups are going into 2 identical printers.

Well to my surprise, using the Pi3 that I was using on the first setup, I started having the exact same issue on the new duet 3. I then grabbed my last Pi 3 I had and swapped only it and everything worked on that setup.

So, with all of that I can only conclude that there is something wrong with the original Pi3 I was using however, I do not know what.

I know not everyone will have extra Duet 3's or SBC's laying around, but this happen to be the fix for me.

Update. After almost a week of messing with it, I got everything working. BLUF: the only thing that has made sense is that there is a problem with my Raspberri Pi.

I started by using bossa and reflashing the duet 3... that didn't fix the problem.
I remembered I had a few Raspberri Pi 3 laying around from other projects as well as I had purchased another duet 3 for my other printer. I decided to swap out one thing at a time, starting with a new SD card.
I then used the new SD card and started with a fresh Duet Pi image. I was still getting errors/incompatble firmware and Error: M997: Failed to find IAP file /opt/dsf/sd/sys/Duet3_SBCiap_MB6HC.bin
I went back to follow the https://duet3d.dozuki.com/Wiki/Getting_Started_With_Duet_3#Section_Updating_Duet_3_from_RRF3_0_Beta_12_to_3_0_Final_via_DWC
After following that Wiki, it got rid of the incompaable firmware but still said it was missing the Duet3_SBCiap_MB6HC.bin

I then changed only the Raspberri Pi keeping the same SD card and Duet, and after the sudo updates/upgrades everything was working.

After that I was done with that duet 3 and SBC setup I decided to setup my other new duet 3 and duplicate what I did as both setups are going into 2 identical printers.

Well to my surprise, using the Pi3 that I was using on the first setup, I started having the exact same issue on the new duet 3. I then grabbed my last Pi 3 I had and swapped only it and everything worked on that setup.

So, with all of that I can only conclude that there is something wrong with the original Pi3 I was using however, I do not know what.

I know not everyone will have extra Duet 3's or SBC's laying around, but this happen to be the fix for me.

@Phaedrux the photo didn't update in my response.

Ok, where to begin...

I followed those steps you suggested that was posted on the "getting started with Duet 3". I had no change what so ever.

I then decided to try resetting the board by windows/bossa flash. I flashed the board with the Duet3Firmware_MB6HC.bin that was with the RRF 3.2, then I tried to update firmware again using the link and instructions on the Getting Started, I got an error:
M997 S0
Error: M997: Failed to find IAP file /opt/dsf/sd/sys/Duet3_SBCiap_MB6HC.bin

I then decided to try all over again but this time back to 3.1.1
I flashed Duet3Firmware_MB6HC.bin from 3.1.1 to the board via bossa. This time when DWC restarted all my config.g items started working: the printer status, tools, temp chart(see picture)

After seeing the change in DWC with config, I then sent M122 and got the following:

m122
=== Diagnostics ===
RepRapFirmware for Duet 3 MB6HC version 3.1.1 running on Duet 3 MB6HC v0.6 or 1.0 (SBC mode)
Board ID: 08DJM-956L2-G43S4-6J9D4-3SN6N-TU66G
Used output buffers: 1 of 40 (10 max)
=== RTOS ===
Static ram: 154604
Dynamic ram: 162584 of which 44 recycled
Exception stack ram used: 224
Never used ram: 75760
Tasks: NETWORK(ready,1980) HEAT(blocked,820) CanReceiv(suspended,3820) CanSender(suspended,1488) CanClock(blocked,1436) TMC(blocked,204) MAIN(running,5048) IDLE(ready,76)
Owned mutexes:
=== Platform ===
Last reset 00:06:19 ago, cause: reset button
Last software reset time unknown, reason: User, spinning module GCodes, available RAM 91776 bytes (slot 3)
Software reset code 0x0003 HFSR 0x00000000 CFSR 0x00000000 ICSR 0x0444a000 BFAR 0x00000000 SP 0xffffffff Task MAIN
Error status: 0
MCU temperature: min 32.9, current 35.0, max 35.2
Supply voltage: min 13.4, current 13.7, max 13.9, under voltage events: 0, over voltage events: 0, power good: yes
12V rail voltage: min 12.1, current 12.1, max 12.2, under voltage events: 0
Driver 0: standstill, reads 20121, writes 14 timeouts 0, SG min/max 0/0
Driver 1: standstill, reads 20121, writes 14 timeouts 0, SG min/max 0/0
Driver 2: standstill, reads 20122, writes 14 timeouts 0, SG min/max 0/0
Driver 3: standstill, reads 20122, writes 14 timeouts 0, SG min/max 0/0
Driver 4: standstill, reads 20126, writes 11 timeouts 0, SG min/max 0/0
Driver 5: standstill, reads 20126, writes 11 timeouts 0, SG min/max 0/0
Date/time: 2021-01-21 22:17:17
Slowest loop: 3.85ms; fastest: 0.15ms
=== Storage ===
Free file entries: 10
SD card 0 not detected, interface speed: 37.5MBytes/sec
SD card longest read time 0.0ms, write time 0.0ms, max retries 0
=== Move ===
Hiccups: 0(0), FreeDm: 375, MinFreeDm: 375, MaxWait: 0ms
Bed compensation in use: none, comp offset 0.000
=== MainDDARing ===
Scheduled moves: 0, completed moves: 0, StepErrors: 0, LaErrors: 0, Underruns: 0, 0 CDDA state: -1
=== AuxDDARing ===
Scheduled moves: 0, completed moves: 0, StepErrors: 0, LaErrors: 0, Underruns: 0, 0 CDDA state: -1
=== Heat ===
Bed heaters = 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1, chamberHeaters = -1 -1 -1 -1
=== GCodes ===
Segments left: 0
Movement lock held by null
HTTP* is ready with "M122" in state(s) 0
Telnet is idle in state(s) 0
File is idle in state(s) 0
USB is idle in state(s) 0
Aux is idle in state(s) 0
Trigger* is idle in state(s) 0 0, running macro
Queue is idle in state(s) 0
LCD is idle in state(s) 0
SBC is idle in state(s) 0
Daemon* is idle in state(s) 0
Aux2 is idle in state(s) 0
Autopause is idle in state(s) 0
Code queue is empty.
=== Network ===
Slowest loop: 1.03ms; fastest: 0.01ms
Responder states: HTTP(0) HTTP(0) HTTP(0) HTTP(0) HTTP(0) HTTP(0) FTP(0) Telnet(0), 0 sessions Telnet(0), 0 sessions
HTTP sessions: 0 of 8

• Ethernet -
  State: disabled
  Error counts: 0 0 0 0 0
  Socket states: 0 0 0 0 0 0 0 0
  === CAN ===
  Messages sent 1515, longest wait 0ms for type 0
  === Linux interface ===
  State: 0, failed transfers: 1
  Last transfer: 18ms ago
  RX/TX seq numbers: 25619/15050
  SPI underruns 1, overruns 1
  Number of disconnects: 0
  Buffer RX/TX: 0/0-0
  === Duet Control Server ===
  Duet Control Server v3.2.0
  Trigger:
  Buffered code: T0 ; select first tool
  ==> 24 bytes
  Executing macro config.g, started by system

Next stack level
Code buffer space: 4096
Configured SPI speed: 8000000 Hz
Full transfers per second: 39.69
Maximum length of RX/TX data transfers: 3168/620

The part that stood out to me was the:
RepRapFirmware for Duet 3 MB6HC version 3.1.1 running on Duet 3 MB6HC v0.6 or 1.0 (SBC mode)

It now said SBC Mode.
After seeing this I tried updating the firmware to 3.2 again using the: Updating Duet 3 from RRF3.0 Beta 12 to 3.0 Final via DWC and am still getting the error:
M997 S0
Error: M997: Failed to find IAP file /opt/dsf/sd/sys/Duet3_SBCiap_MB6HC.bin

I feel like I got one step forward then one step back(a different step)

I believe I will now try the Sudo apt-get update/upgrade again and if that doesn't work i'm thinking of starting fresh with the RPI immage.

Any thoughts?

All, I have a Duet3 MB 6HC with Rpi 3B V1.2 running SBC mode. I was installing it into an FT-6 printer.

The problem I'm having seems like my config file and firmware are not being read during startup, as I do not have any tools, axis showing in DWC.

I first set it up a few months ago on 3.1.1 and the only difference was that the status would say "idle" Mode: FFF.
I was able to send commands to manually home axis even though they were not showing in DWC.

Last night I Sudo apt-get update and upgrade to 3.2. thinking maybe the updated firmware might be a fix. Now I'm getting firmware incompatible. I even went back to the RRF configurator and created a new file from scratch with no luck. Any help would be appreciated, I've gone through wiki after wiki and I feel like I'm going down a rabbit hole chasing my tail.

Please see the photos of my DWC as well as my m122 as requested by @Phaedrux M98 P"config.g" not doing anything today.
Prior to my update last night when it would connect, I was getting the exact same Bad commands just like on this post by @sol88
https://forum.duet3d.com/topic/20670/problems-geting-started-with-duet-web-control?_=1611026026749

m122
=== Diagnostics ===
RepRapFirmware for Duet 3 MB6HC v0.6 or 1.0 version 3.0beta12 running on Duet 3 MB6HC
Board ID: 08DJM-956L2-G43S4-6J9D4-3SN6N-TU66G
Used output buffers: 1 of 32 (4 max)
=== RTOS ===
Static ram: 122240
Dynamic ram: 172460 of which 0 recycled
Exception stack ram used: 216
Never used ram: 98300
Tasks: NETWORK(ready,2044) HEAT(blocked,1208) CanReceiv(suspended,3804) CanSender(suspended,1480) CanClock(blocked,1428) TMC(blocked,232) MAIN(running,4212) IDLE(ready,200)
Owned mutexes:
=== Platform ===
Last reset 00:00:22 ago, cause: software
Last software reset at 2021-01-18 23:27, reason: Unknown, spinning module Platform, available RAM 98236 bytes (slot 3)
Software reset code 0x0010 HFSR 0x00000000 CFSR 0x00000000 ICSR 0x0444a000 BFAR 0x00000000 SP 0xffffffff Task 0x4e49414d
Error status: 0
Free file entries: 10
SD card 0 not detected, interface speed: 37.5MBytes/sec
SD card longest block write time: 0.0ms, max retries 0
MCU temperature: min 23.7, current 24.1, max 24.2
Supply voltage: min 23.9, current 24.0, max 24.0, under voltage events: 0, over voltage events: 0, power good: yes
12V rail voltage: min 12.1, current 12.1, max 12.1, under voltage events: 0
Driver 0: standstill, reads 37854, writes 14 timeouts 0, SG min/max 0/0
Driver 1: standstill, reads 37855, writes 14 timeouts 0, SG min/max 0/0
Driver 2: standstill, reads 37856, writes 14 timeouts 0, SG min/max 0/0
Driver 3: standstill, reads 37857, writes 14 timeouts 0, SG min/max 0/0
Driver 4: standstill, reads 37861, writes 11 timeouts 0, SG min/max 0/0
Driver 5: standstill, reads 37862, writes 11 timeouts 0, SG min/max 0/0
Date/time: 2021-01-18 23:27:57
Slowest loop: 5.98ms; fastest: 0.25ms
=== Move ===
Hiccups: 0, FreeDm: 375, MinFreeDm: 375, MaxWait: 0ms
Bed compensation in use: none, comp offset 0.000
=== MainDDARing ===
Scheduled moves: 0, completed moves: 0, StepErrors: 0, LaErrors: 0, Underruns: 0, 0
=== AuxDDARing ===
Scheduled moves: 0, completed moves: 0, StepErrors: 0, LaErrors: 0, Underruns: 0, 0
=== Heat ===
Bed heaters = 0 -1 -1 -1, chamberHeaters = -1 -1
Heater 1 is on, I-accum = 0.0
=== GCodes ===
Segments left: 0
Stack records: 1 allocated, 0 in use
Movement lock held by null
http* is ready with "M122" in state(s) 0
telnet is idle in state(s) 0
file is idle in state(s) 0
serial is idle in state(s) 0
aux is idle in state(s) 0
daemon* is idle in state(s) 0
queue is idle in state(s) 0
lcd is idle in state(s) 0
spi is idle in state(s) 0
autopause is idle in state(s) 0
Code queue is empty.
=== Network ===
Slowest loop: 0.52ms; fastest: 0.01ms
Responder states: HTTP(0) HTTP(0) HTTP(0) HTTP(0) HTTP(0) HTTP(0) FTP(0) Telnet(0) Telnet(0)
HTTP sessions: 0 of 8

• Ethernet -
  State: 0
  Socket states: 0 0 0 0 0 0 0 0
  === CAN ===
  Messages sent 26, longest wait 0ms for type 0
  === Linux interface ===
  State: 1, failed transfers: 1
  Last transfer: 19ms ago
  RX/TX seq numbers: 248/248
  SPI underruns 1, overruns 1
  Number of disconnects: 0
  Buffer RX/TX: 0/0-0
  === Duet Control Server ===
  Duet Control Server v3.2.0
  Code buffer space: 4096
  Configured SPI speed: 8000000 Hz
  Full transfers per second: 28.16
  Maximum length of RX/TX data transfers: 3020/768

Config.g:

; Configuration file for Duet 3 (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.2.1 on Mon Jan 18 2021 22:45:39 GMT-0500 (Eastern Standard Time)

; General preferences
G90 ; send absolute coordinates...
M83 ; ...but relative extruder moves
M550 P"Duet 3" ; set printer name

; Drives
M569 P0.0 S1 ; physical drive 0.0 goes forwards
M569 P0.1 S1 ; physical drive 0.1 goes forwards
M569 P0.2 S1 ; physical drive 0.2 goes forwards
M569 P0.3 S1 ; physical drive 0.3 goes forwards
M584 X0.0 Y0.1 Z0.2 E0.3 ; set drive mapping
M350 X16 Y16 Z16 E16 I1 ; configure microstepping with interpolation
M92 X80.00 Y80.00 Z400.00 E420.00 ; set steps per mm
M566 X900.00 Y900.00 Z60.00 E120.00 ; set maximum instantaneous speed changes (mm/min)
M203 X6000.00 Y6000.00 Z180.00 E1200.00 ; set maximum speeds (mm/min)
M201 X500.00 Y500.00 Z20.00 E250.00 ; set accelerations (mm/s^2)
M906 X800 Y800 Z800 E800 I30 ; set motor currents (mA) and motor idle factor in per cent
M84 S30 ; Set idle timeout

; Axis Limits
M208 X0 Y0 Z0 S1 ; set axis minima
M208 X600 Y300 Z400 S0 ; set axis maxima

; Endstops
M574 X1 S1 P"io0.in" ; configure active-high endstop for low end on X via pin io0.in
M574 Y1 S1 P"io1.in" ; configure active-high endstop for low end on Y via pin io1.in
M574 Z1 S1 P"io7.in" ; configure active-high endstop for low end on Z via pin io7.in

; Z-Probe
M558 P0 H5 F120 T6000 ; disable Z probe but set dive height, probe speed and travel speed
M557 X15:215 Y15:195 S20 ; define mesh grid

; Heaters
M308 S0 P"temp0" Y"thermistor" T100000 B4138 ; configure sensor 0 as thermistor on pin temp0
M950 H0 C"out0" T0 ; create bed heater output on out0 and map it to sensor 0
M307 H0 B1 S1.00 ; enable bang-bang mode for the bed heater and set PWM limit
M140 H0 ; map heated bed to heater 0
M143 H0 S120 ; set temperature limit for heater 0 to 120C
M308 S1 P"temp1" Y"thermistor" T100000 B4138 ; configure sensor 1 as thermistor on pin temp1
M950 H1 C"out1" T1 ; create nozzle heater output on out1 and map it to sensor 1
M307 H1 B0 S1.00 ; disable bang-bang mode for heater and set PWM limit
M143 H1 S280 ; set temperature limit for heater 1 to 280C

; Fans
M950 F0 C"out4" Q500 ; create fan 0 on pin out4 and set its frequency
M106 P0 S0 H-1 ; set fan 0 value. Thermostatic control is turned off
M950 F1 C"out5" Q500 ; create fan 1 on pin out5 and set its frequency
M106 P1 S1 H1 T45 ; set fan 1 value. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 F0 ; define tool 0
G10 P0 X0 Y0 Z0 ; set tool 0 axis offsets
G10 P0 R0 S0 ; set initial tool 0 active and standby temperatures to 0C

; Custom settings are not defined

; Miscellaneous
T0 ; select first tool

@sol88 I have been having the same issue and I am stuck. I've tried the config tool multiple time and it looks like everything is setup but getting the same bad commands as well as no tools or anything else showing in DWC.

The only thing I did to try to fix since is in each .g file to include the config.g was to delete any line that started with a semicolon. This got rid of the bad commands but now it says incompatible firmware even after update through sudo CMD to 3.2