i have also a not working right jogwheel which is very frustrating when sou see the promo video's where scratching from here to moon and backwards is showed, i am not a scratcher but an oldskool dj just wanted to swop my denon 3500s for something newer and get rit of changing cd's all the time.
However if i toss my contoller on it's back the jogwheel's are hanging downwards and guess what happened.... yes...the right wheel is working again, the load lamp is off and a cue can be made without it sticking in the scatch mode. so you might try this also it might help you to find out where the problem comes from.
next step I think i ll mount it to the ceiling to keep it working.
It sounds Stupid but toyota is calling it cars back but Ni is not so far yet. Sometimes i wished i had waited for the new denon 6000 controller. Anyway my dealer offered to return to him because he might have some trick(s) to help things back on track, it cost some extra free time and traveltime but hopefully it will help.