Unfortunately I know exactly what is going on there. There is a known but rare issue (100% my fault) where the encoder starts working backwards. The solution is to solder one of the pins on the encoder board to ground which forces the encoder to only work in the correct direction.
If you feel up for modifying your encoder like that it should fix the issue, and if not I can modify one for you and send it to you ASAP. We’re still not sure why it happens to some boards and why it happens when it happens, but the fix seems to work reliably.