Considering that only people with the Ender 5 1.1.5 silent boards have so far run into this, I'd say it sounds more like either a firmware or a printer batch issue. As I already said, based on the logs that were shared so far, OctoPrint is sending the commands it needs to send. Something on the printer's side then stops doing what these commands say and does something else instead. Either that, or the commands don't go through correctly (undervoltage?) in which case it would be fairly unexpected to only affect one single axis however.
The case of the problem wandering along with the motor sounds like a hardware issue, could be that this only looks like the same issue but is an actual mechanical problem.
Different firmware might be an idea, and I'd also suggest to replicate the experiment of swapping the X/Y axis to see if the problem moves with the motor or stays on the axis.
SD card printing doesn't involve checksums, so switching those off temporarily could also give insights, in case there's a parser bug in the firmware regarding the checksums.
Also check for undervoltage and increased communication errors.