I think that this could be a good suggestion to try next. There does seem to be something encoder related going on and that seems to be the outstanding encoder related issue.
The offiending pin is this one, closest to where it says C1:
The fix is to add a little solder bridge over to the end of the capacitor next to it, if you want to try it.
I can also send you some modified boards for testing if you are OK with waiting for them to arrive.