Unfortunately some setups seem to suffer problems others do not. Things that may help to overcome the issue…
- Make sure you are running at least version 3.2.2 on both ends (especially on the rPi), this version has a fix that helps a lot woth noise on the transfer ready line.
- Keep the cable between the boards as short as possible and use a ribbon cable (or possibly twisted pairs), shielding of the cable may help. The shorter the better. dc42 recommends less than 15cm
- Keep the cable routing away from other cables especially power supply and switched heater wiring
- Ensure that there is a very good common ground connection between the rPi and main board (the connectors in the ribbon cable may not be enough).
- Ensure that the rPi has a very good 5V power supply.
- There are a number of threads on the Duet forum that may help: https://forum.duet3d.com/topic/21834/restart-duetcontrolserver-sbc/5 https://forum.duet3d.com/topic/21357/duet2-wifi-duex5-and-sbc?_=1614522809264
Gloomyandy runs two SBC based printers (one STM32 one LPC) and has no issues with the connection between the boards. In both cases he has the rPi mounted “back to back” with the main board and run a very short ribbon cable that does not run over the main board and that forms a “U” shape between the two boards.