Try replacing your battery for starters. A few weeks ago I got called in because last years robot wasn't working - two motors turned just fine, but the other two didn't. Very odd problem that I spent an hour or so scratching my head over. We swapped Jags in an out, redid wiring, replaced the digital side car... it was a mess. Finally I decided to start completely over with the obvious things I assumed they had checked before calling me over... to find the battery extremely low (somewhere around 9 V, IIRC). Replaced it, and everything worked fine.
If the battery isn't your problem, you may need to calibrate your PWM inputs. You can find instructions for that on page 2 of the "Getting Started (MDL-BDC)" link here:
http://www.luminarymicro.com/jaguar