There was a request for a more clear and easy to find set of instructions for how to solder the encoder boards (the previous answer was buried in a thread and not easy to search for or find) so this is duplicate information but in a more searchable way.
The issue is that the encoder chips have a pin which can be used to set the direction that the encoder reads (IE is rotating counter clockwise positive or clockwise positive). We left this pin unconnected (our mistake) which seems to under some circumstances lead to the encoder detecting rotation in the wrong direction. It seems to be somehow related to static electricity or humidity or something like that.
The offending 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.
If you have this issue and try to fix it and mess up the board, or if you don’t want to try it at all I can send you some free encoder boards which are already modified.