@phaedrux Yeah, that's what I was afraid you'd say Now I've got to disassemble the printer to get access to the usb port...

I'm doing a yum upgrade, and everything worked, except the reprapfirmware:

pi@duet3:~ $ sudo apt upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages were automatically installed and are no longer required:
  libllvm8 libxss1 rpi-eeprom-images
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Do you want to continue? [Y/n] y
Setting up reprapfirmware (3.4-b7-2) ...

Progress: [ 33%] [###################.......................................]

Here's the output from M122, am I making too large a jump in versions or something?

M122
=== Diagnostics ===
RepRapFirmware for Duet 3 MB6HC v0.6 or 1.0 version 3.01-RC2 running on Duet 3 MB6HC
Board ID: 08DJM-956L2-G43S8-6J9DA-3SD6J-1V3QF
Used output buffers: 1 of 40 (4 max)

Solved, or, no longer seeing the issue - I THINK it has something to do with the heater model which was coming in from config-override.g. I manually entered the correct model (because M500 wasn't saving anything other than empty values), forced the config-override to load on reboot, and... all my problems have gone away. (well, except for a inconsistent z-probe offset, but that's on me)

Could it have something to do with running off of the virtual sd card on the SBC, and not off of a dedicated card on the board itself?

Same issue:

M122

=== Diagnostics ===
RepRapFirmware for Duet 3 MB6HC v0.6 or 1.0 version 3.01-RC2 running on Duet 3 MB6HC
Board ID: 08DJM-956L2-G43S8-6J9DA-3SD6J-1V3QF
Used output buffers: 1 of 40 (13 max)
=== RTOS ===
Static ram: 153912
Dynamic ram: 158500 of which 44 recycled
Exception stack ram used: 216
Never used ram: 80544
Tasks: NETWORK(ready,1972) HEAT(blocked,1196) CanReceiv(suspended,3820) CanSender(suspended,1488) CanClock(blocked,1436) TMC(blocked,212) MAIN(running,4544) IDLE(ready,76)
Owned mutexes:
=== Platform ===
Last reset 00:05:31 ago, cause: software
Last software reset at 2020-02-27 00:24, reason: Memory protection fault, spinning module GCodes, available RAM 80160 bytes (slot 1)
Software reset code 0x4163 HFSR 0x00000000 CFSR 0x00000082 ICSR 0x0443a804 BFAR 0x171f0b9b SP 0x20417814 Task 0x4e49414d
Stack: 00424583 0040110e 610d0000 00000000 00000000 00000000 00000000 00000000 ffffffff 2042e520 00000000
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 35.1, current 35.4, max 35.4
Supply voltage: min 23.6, current 23.7, max 23.7, under voltage events: 0, over voltage events: 0, power good: yes
12V rail voltage: min 11.9, current 11.9, max 12.0, under voltage events: 0
Driver 0: standstill, reads 5689, writes 0 timeouts 0, SG min/max not available
Driver 1: standstill, reads 5689, writes 0 timeouts 0, SG min/max not available
Driver 2: standstill, reads 5689, writes 0 timeouts 0, SG min/max not available
Driver 3: standstill, reads 5689, writes 0 timeouts 0, SG min/max not available
Driver 4: standstill, reads 5688, writes 0 timeouts 0, SG min/max not available
Driver 5: standstill, reads 5689, writes 0 timeouts 0, SG min/max not available
Date/time: 2020-02-27 00:30:09
Slowest loop: 2.16ms; fastest: 0.13ms
=== 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
=== AuxDDARing ===
Scheduled moves: 0, completed moves: 0, StepErrors: 0, LaErrors: 0, Underruns: 0, 0
=== 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
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: 0.86ms; 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
  Error counts: 0 0 0 0 0
  Socket states: 0 0 0 0 0 0 0 0
  === CAN ===
  Messages sent 57, longest wait 0ms for type 0
  === Linux interface ===
  State: 0, failed transfers: 0
  Last transfer: 16ms ago
  RX/TX seq numbers: 7674/10552
  SPI underruns 0, overruns 0
  Number of disconnects: 0
  Buffer RX/TX: 0/0-0
  === Duet Control Server ===
  Duet Control Server v1.2.4.0
  Code buffer space: 4096
  Configured SPI speed: 2000000 Hz
  Full transfers per second: 31.73

Not sure if it's in any way related, but M500 doesn't seem to want to save autotune results either, this is what the M500 writes to config-override.g:

; config-override.g file generated in response to M500 at 2020-02-27 00:43

; Heater model parameters
M307 H0 A C D S V B0
M307 H1 A C D S V B0
; Workplace coordinates

Having a weird issue whenever I start a print job on my Duet3. The bed heater starts warming, but within a couple of seconds I get a bunch of messages on the UI that there's been a reset and the job stops.

Using M122, I get the following diagnostics:

=== Diagnostics ===
RepRapFirmware for Duet 3 MB6HC v0.6 or 1.0 version 3.0 running on Duet 3 MB6HC
Board ID: 08DJM-956L2-G43S8-6J9DA-3SD6J-1V3QF
Used output buffers: 1 of 32 (5 max)
=== RTOS ===
Static ram: 152720
Dynamic ram: 149628 of which 20 recycled
Exception stack ram used: 216
Never used ram: 90632
Tasks: NETWORK(ready,1984) HEAT(blocked,1200) CanReceiv(suspended,3808) CanSender(suspended,1476) CanClock(blocked,1424) TMC(blocked,212) MAIN(running,4476) IDLE(ready,160)
Owned mutexes:
=== Platform ===
Last reset 00:03:33 ago, cause: software
Last software reset at 2020-02-26 17:51, reason: Memory protection fault, spinning module GCodes, available RAM 90248 bytes (slot 0)
Software reset code 0x4163 HFSR 0x00000000 CFSR 0x00000082 ICSR 0x0444a804 BFAR 0x2235040a SP 0x20417314 Task 0x4e49414d
Stack: 00421347 004006da 61000000 00000000 ffffffff 20415c30 0000017c 2043bec6 00000000 2043bd4e 2043bc98 00000001 00000018 00000001 00000000 00000000 0045484d 00000001 20428540 00000001 00000000 00000000 2042b758
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 35.4, current 35.5, max 36.0
Supply voltage: min 23.4, current 23.5, max 23.5, under voltage events: 0, over voltage events: 0, power good: yes
12V rail voltage: min 11.9, current 12.0, max 12.0, under voltage events: 0
Driver 0: standstill, reads 5381, writes 14 timeouts 0, SG min/max 0/0
Driver 1: standstill, reads 5382, writes 14 timeouts 0, SG min/max 0/0
Driver 2: standstill, reads 5382, writes 14 timeouts 0, SG min/max 0/0
Driver 3: standstill, reads 5383, writes 14 timeouts 0, SG min/max 0/0
Driver 4: standstill, reads 5386, writes 11 timeouts 0, SG min/max 0/0
Driver 5: standstill, reads 5384, writes 14 timeouts 0, SG min/max 0/0
Date/time: 2020-02-26 17:55:30
Slowest loop: 2.23ms; fastest: 0.08ms
=== 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
=== AuxDDARing ===
Scheduled moves: 0, completed moves: 0, StepErrors: 0, LaErrors: 0, Underruns: 0, 0
=== Heat ===
Bed heaters = 0 -1 -1 -1 -1 -1 -1 -1 -1, chamberHeaters = -1 -1 -1 -1
=== 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: 0.46ms; 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
  Error counts: 0 0 0 0 0
  Socket states: 0 0 0 0 0 0 0 0
  === CAN ===
  Messages sent 852, longest wait 0ms for type 0
  === Linux interface ===
  State: 0, failed transfers: 0
  Last transfer: 13ms ago
  RX/TX seq numbers: 28973/6817
  SPI underruns 0, overruns 0
  Number of disconnects: 0
  Buffer RX/TX: 0/0-0
  === Duet Control Server ===
  Duet Control Server v1.2.4.0
  Code buffer space: 4096
  Configured SPI speed: 2000000 Hz
  Full transfers per second: 30.51