@fcwilt @fcwilt I was testing a ton of different stuff and I ended up commenting those out.
I just found the problem...
;Fan
M950 F0 C"fan0" ;Create Fan 0
M106 P0 S0
M950 F1 C"fan1" ;Create Fan 1
M106 P1 S1
The "Create Fan 0" and the "Create Fan 1" was not commented. I have no idea how this happened, because I certainly didn't change it after doing the firmware update.
Well I feel like I wasted your time, but thanks for the help!