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Mike -- Sorry for the troubles. This happens in any field when you try something new, whether it is new gear or new techniques.
This is the first I've heard about the incompatibility of the batteries. I've experienced a few hiccups in the past using after market batteries in the 60D, but nothing catastrophic, just switch them, or put in 5D2 and they work, even mixed with Canon.
You may have a faulty grip as well, since the AA's didn't work.
It will all work out, but it my be annoying for a while. I've had it go both ways -- with both new and used. Mostly both new AND used are great! But sometimes they can both crap out.