[Chris Hibner]

Are you doing any encoder resets? (In LabVIEW, there is a Reset Encoder vi that resets the encoder counts to 0 and stops the encoder, you then need to do an Encoder Start. I'm assuming there are equivalent methods of doing this in C++ and Java.)

I found a bug with the Encoder Reset / Encoder Start / Encoder Stop functionality in the 2012 firmware. The bug caused it to act exactly as you're describing. We lost days trying to track that down.