I have really been tested the past few days doing a controller board swop out on my Ender 6.
The last issue I had was that while running a print from OctoPrint , the print head would randomly stop/pause for a while and then continue on again. Also the print speed would just slow down to a crawl on some layers and then speed up again on the next. All this of course would leave nasty artifacts and ruin the print.
After a lot of fault diagnosis, looking at the Octoprint config and then the serial comms config of the SKR Mini E3 V2 board, I just couldn't pin it down.I even installed Ferite cores on the comms cables to try and resolve noise, but nothing helped.
It turned out the fault lay with another piece of hardware I swopped out, but didn't think of suspecting... I replaced the stock DGUS touch display of the Ender 6 with a BTT TFT35 E3 V3 display to match the SKR board. This was an old display I had on the shelf to install in my Ender 3, but never did. During all my tests I used the Marlin LCD simulator mode of the display as this was known to me.
Having discussed the fault on a facebook group, it dawned on me that maybe this display might be causing issues on it serial interface. I had both the standard LCD and the Serial TFT interface connected between the board and display so I could switch between Touch screen and Marlin LCD modes on the fly. I disconnected the serial interface (which doesn't effect the Marlin LCD mode) and ran a print. No issues...
I realised that maybe I should update the firmware of the display as well since it was a very early model still with the factory config on it. It was quite easy to do and after it finished I connected the serial port again and ran a print. Again no issues...
At the moment I'm running another print and if this one is all good then it seems I might have found the issue.
I am cautiously optimistic and will let you know if all went well.
Thought I might just share my experiences.