For others who find this thread: I just installed beta 3.3 and it's working correctly now, looks like root cause was in can communications.

@dc42 @jballard86 Either of you ever figure this out yet? i just setup with 2 clearpath servos i see 0 hiccups but the layer shifts are real! i'm on version RRF 3.2 via duet3 + Pi4 SBC.

For purposes of ease you can consider the wiring to be a 24v PS powering the duet with an e-stop on the 110v AC hot line to the Powersupply. All voltages have been tested and are stable and good.
Powersupply is Meanwell, not a shoddy no name brand.
Reason for simplifying wiring explanation (https://photos.app.goo.gl/xwvkHzTZuaX2JA2P6) Don't judge not fully wire-managed yet

The SBC currently powered via a 110v to 5v 3A USB-c "wall wart"; to be changed to a dedicated 5v powersupply once I rebuild the cable between duet3 and Pi.

The Duet only has the Internal 5v Enable jumper set: i.e. SBC -> 5v, and 5v -> SBC and not jumpered.

I am using the cable sent with the Duet3 for interboard communications.

Will get M122 and enable monitoring and get some thing uploaded shortly.

Here is a copy of the M122

I tried again to capture before it went into Warn loop but even sitting with wireless keyboard in hand to try and stop the process as soon as the loop started it would clear the putty terminal history.

M122 right after boot

M122
=== Diagnostics ===
RepRapFirmware for Duet 3 MB6HC version 3.3beta running on Duet 3 MB6HC v1.01 or later (SBC mode)
Board ID: 08DJM-956L2-G43S8-6J1D8-3S46S-9V2LF
Used output buffers: 1 of 40 (10 max)
=== RTOS ===
Static ram: 149784
Dynamic ram: 59500 of which 100 recycled
Never used RAM 141288, free system stack 178 words
Tasks: Linux(ready,149) HEAT(blocked,299) CanReceiv(blocked,865) CanSender(blocked,365) CanClock(blocked,326) TMC(blocked,50) MAIN(running,1260) IDLE(ready,20)
Owned mutexes: HTTP(MAIN)
=== Platform ===
Last reset 01:05:58 ago, cause: power up
Last software reset details not available
Error status: 0x00
Aux0 errors 0,0,0
Aux1 errors 0,0,0
MCU temperature: min 21.7, current 33.4, max 33.5
Supply voltage: min 24.4, current 24.5, max 24.5, under voltage events: 0, over voltage events: 0, power good: yes
12V rail voltage: min 12.2, current 12.2, max 12.3, under voltage events: 0
Driver 0: position 0, standstill, reads 15592, writes 11 timeouts 0, SG min/max 0/0
Driver 1: position 0, standstill, reads 15592, writes 11 timeouts 0, SG min/max 0/0
Driver 2: position 0, standstill, reads 15586, writes 17 timeouts 0, SG min/max 0/0
Driver 3: position 0, standstill, reads 15586, writes 17 timeouts 0, SG min/max 0/0
Driver 4: position 0, standstill, reads 15592, writes 11 timeouts 0, SG min/max 0/0
Driver 5: position 0, standstill, reads 15592, writes 11 timeouts 0, SG min/max 0/0
Date/time: 2021-01-30 19:40:17
Slowest loop: 0.63ms; fastest: 0.05ms
=== 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 ===
DMs created 125, maxWait 0ms, bed compensation in use: none, comp offset 0.000
=== MainDDARing ===
Scheduled moves 0, completed moves 0, hiccups 0, stepErrors 0, LaErrors 0, Underruns [0, 0, 0], CDDA state -1
=== AuxDDARing ===
Scheduled moves 0, completed moves 0, hiccups 0, stepErrors 0, LaErrors 0, Underruns [0, 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 doing "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
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.
=== CAN ===
Messages queued 15761, send timeouts 0, received 47228, lost 0, longest wait 2ms for reply type 6049, peak Tx sync delay 172, free buffers 48 (min 47)
=== SBC interface ===
State: 4, failed transfers: 0
Last transfer: 1ms ago
RX/TX seq numbers: 3432/3432
SPI underruns 0, overruns 0
Number of disconnects: 1, IAP RAM available 0x2d584
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: 35.81
Maximum length of RX/TX data transfers: 4756/32

config.g

; Configuration file for Duet 3 (firmware version 3)
; executed by the firmware on start-up
;


; General preferences
G90                                          		; send absolute coordinates...
M83                                          		; ...but relative extruder moves
M550 P"Duet 3"                          			; set printer name
G21 												; Set units to Millimeters
G4 S1												; wait for Daughter Boards to start

; Drives
M569 P40.0 S1 R1 					             	; External driver board (40): driver 0 (X) goes Backwards ( T1.25:1.25:1.25:1.25 )
M569 P41.0 S1 R1					         		; External driver board (41): driver 0 (Y) goes Backwards
M569 P20.0 S1 R1                               		; External Toolboard (20): driver 0 (E) goes Backwards 
M569 P2 S0 D3 H35 V35 S0 							; physical drive 2(Z1) with StealthChop (D,H,V) and goes forwards
M569 P3 S1 D3 H35 V35 S1 							; physical drive 3(Z2) with StealthChop (D,H,V) and goes Backwards
;M915 P2 T32                                        ; additional setting for SealthChop on Drive 2
;M915 P3 T32                                        ; additional setting for SealthChop on Drive 3
M584 X40.0 Y41.0 Z2:3 E20.0        					; set drive mapping
M350 E16 Z16 I1                      				; configure microstepping with interpolation
M350 X1 Y1 I0										; configure no microstepping without interpolation
M92 X200 Y200 Z1200 E415							; set steps per mm E392.5507
M566 X900.00 Y900.00 Z150.00 E300.00          		; set maximum instantaneous speed changes (mm/min)
M203 X9000.00 Y9000.00 Z700.00 E3000.00    			; set maximum speeds (mm/min)
M201 X5000.00 Y5000.00 Z1500.00 E2000.00     		; set accelerations (mm/s^2)
M906 Z3500 E600 I10                					; set motor currents (mA) and motor idle factor in percent
M84 S3                                       		; Set idle timeout

; Axis Limits
M208 X-260:266.7 Y-135:138.5 Z-.5:310.73          	; set axis maxima

; Z-Probe
M558 P9 C"20.io0.in" H5 R.02 F120 T3000				; defines probe type, pin, Starting height, .02 seconds settle time, FeedRate, Rapid Speed (mm/min)
M950 S0 C"20.io0.out"								; defines GPIO servo pin for BLTouch Control
G31 X-4.25 Y46 Z4.12								; defines Probe offset
M557 X-132:108 Y-97:90 S20:20                   	; define mesh grid size, and probe point spacing 
M376 H2												; Mesh bed compensation taper, tapers off adjustments by specified height in mm

; Filament Sensor
;M591 D0 P2 C"20.io2.in" S1							; defiens filament monitor on Extruder 0, simple switch: low when present, no toolboard io2, works when printing from SD Card

; Endstops
M574 X1 S1 P"io0.in"                                ; set X minimum endstop to microswitch on io0
M574 X2 S1 P"io3.in"                                ; set X maximum endstop to microswitch on io2
M574 Y1 S1 P"io5.in"                                ; set Y minimum endstop to microswitch on io5
M574 Y2 S1 P"io7.in"                                ; set Y maximum endstop to microswitch on io7
M574 Z2 S1 P"io8.in"                                ; set X minimum endstop to microswitch on io8

; Heaters
M308 S0 P"temp0" Y"thermistor" T100000 B3950 H2		; configure sensor 0 as thermistor on pin temp0 and adjust ADC High Gain
M950 H0 C"out0" Q20 T0                      		; create bed heater output on out0 and map it to sensor 0
M307 H0 B0 S0.50                 	         		; disable bang-bang mode for the bed heater and set PWM limit (0-1)
M140 H0                                      		; map heated bed to heater 0
M143 H0 S120                                 		; set temperature limit for heater 0 to 120C
M308 S1 P"20.temp0" Y"thermistor" T1073 B-450		; configure sensor 1 as PT1000 on pin temp0 on tool board and adjust ADC Low Gain (M308 S1 P"20.temp0" Y"pt1000") (M308 S1 P"20.temp0" Y"thermistor" T1073 B-450)
M950 H1 C"20.out0" 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 S300										; set temperature limit for heater 1 to 300C

; Fans
M950 F0 C"20.out1" Q25000                    		; create fan 0 on Toolboard(20) to out2 and set its frequency
M106 P0 S1 H1 T40            		            	; set fan 0 off, bind to heater 1, triggers on at 50 deg.C Resumes after pause.
M950 F1 C"20.out2" Q10000                       	; create fan 1 on Toolboard(20) to out1 and set its frequency
M106 P1 S0 H-1 R1									; Sets Fan 1 to off with no heater binding
M950 F2 C"!out4" Q25000                         	; create fan 2 on pin out4 and set its frequency
M106 P2 S1 H-1                               		; set fan 2 value. Thermostatic control is turned off

; Tools
M563 P0 D0 H1	                             		; 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
M501                                         		; load saved parameters from non-volatile memory

So even more interesting is that when logging to file it seems to work perfectly fine, but when logging to screen or not logging it goes into a repeat loop of the following so fast i can't stop it from clearing the terminal buffer/history to see the moment of connection messages:

To clarify i'm on a RPi4

[warn] Restarting transfer because the number of maximum retries has been exceeded
[warn] RepRapFirmware got a bad header checksum
[warn] RepRapFirmware got a bad header checksum
[warn] RepRapFirmware got a bad header checksum
[warn] Restarting transfer because the number of maximum retries has been exceeded
[warn] RepRapFirmware got a bad header checksum
[warn] RepRapFirmware got a bad header checksum
[warn] RepRapFirmware got a bad header checksum
[warn] Restarting transfer because the number of maximum retries has been exceeded

Links to Logging files, reminder when logging to file reconnect seems to work.
DCS Log: https://drive.google.com/file/d/17NDBcaRQYxjEPqrZ_QPl8vMmUcj6r2tl/view?usp=sharing

DWC Log: https://drive.google.com/file/d/1yroiSNZnQcucnBYU_UXbI2L2KAhQ3o14/view?usp=sharing

For purposes of ease you can consider the wiring to be a 24v PS powering the duet with an e-stop on the 110v AC hot line to the Powersupply. All voltages have been tested and are stable and good.
Powersupply is Meanwell, not a shoddy no name brand.
Reason for simplifying wiring explanation (https://photos.app.goo.gl/xwvkHzTZuaX2JA2P6) Don't judge not fully wire-managed yet

The SBC currently powered via a 110v to 5v 3A USB-c "wall wart"; to be changed to a dedicated 5v powersupply once I rebuild the cable between duet3 and Pi.

The Duet only has the Internal 5v Enable jumper set: i.e. SBC -> 5v, and 5v -> SBC and not jumpered.

I am using the cable sent with the Duet3 for interboard communications.

Will get M122 and enable monitoring and get some thing uploaded shortly.

So I have setup a power safety interlock for my printer and the SBC is powered separately during testing I found that if the Duet3 board is power cycled and the SBC is not they will not pick back up on communications until the SBC is reset (reset can be as simple as save config.g and click yes to reload dwc) or power cycled.

Currently running 3.3 Beta firmware as it's the only way my clearpath servos work correctly.

Don't know if this is the right place, if it's not let me know.

edit - strike through part was false: that was another issue I was chasing from last night and blended into this one, it takes a full SBC reload / reboot to work again.

For others who find this thread: I just installed beta 3.3 and it's working correctly now, looks like root cause was in can communications.

@dc42 @jballard86 Either of you ever figure this out yet? i just setup with 2 clearpath servos i see 0 hiccups but the layer shifts are real! i'm on version RRF 3.2 via duet3 + Pi4 SBC.