What are you running the batts in? Reason I ask, my Emaxx runs one batt down noticeably more than the other - this is the side that powers the BEC and runs the rx and the servos. I run 7 cell pacs that are "handed" so I always see the same batt take more than the other.

Unless you're running them as a pr like this, there's no reason I can think of that they shouldn't be much closer together and I would suspect a batt prob too. When NiMHs peak, they should be hot - 120-130F, but not so hot that you can't hold them.