Are you absolutely sure the encoder board has no shorts or dry joints and everything is in the correct place?
Do you have access to a multi meter and can check the expected responses as you use the encoders and switches?
Do you have a magnifying glass to examine the solder joints and check fro hairline shorts between tracks and dry joints on pins?
If you have these sorts of errors no amount of software configuration will sort the issue out for you.
You need to be sure that the correct response is present at the main chips pins and that the correct pins are wired back to the correct pins on the Pi.