Just a couple troubleshooting questions:
Do you have an expression or other pedals attached?
Are you using MIDI merge/thru with any other devices?
Are you still using the same Control template? If you have accidentally switched to one that uses encoder simulation, that will send CC data whenever the pots aren't dead center. Super irritating. You can also use the A-Pro editor to see if encoder simulation is being used on your current template.
I believe it's possible to re-flash the firmware. It's downloadable from Roland's website. You could try that if none of these other ideas bear fruit.