I'll run a test this weekend to make sure we did not break something in the 1.4.2 Fw. If it appears to work ok then there must be something wrong with either the encoder or the serializer. If it was a bad encoder port on the serializer I would think you would get 0 counts, not just a lower number. I'll let you know what I find as soon as I run the tests and we will get you working.
Ringo
ok, well that probably tells me it is not the Fw then, I would assume somebody else would have mentioned it by now if it was. This is a weird problem. have you tried using the MOGO command yet? Probably not since you can't get consistent readings but just a thought.
Try this. Just rotate the wheel by hand 1 revolution and see what it returns. I would assume this would be as inconsistent as running with PWM, but who knows, maybe it will be a clue.