I also have this problem. There are several posts related to this same glitch, with no apparent solutions. I have contacted AKAI and they say there are "investigating it". I don't believe it is hardware related, because my jog wheel works fine for everything else, just can't change the track type or program.
I've reloaded the OS, and done the factory reset over and over again, with no success. This is super weird and has made my MPC useless. If anyone figured out how to fix this please post your knowledge!