Lynx Arc's post sounds spot on.
I guess part of the lesson is to avoid running NiMH batteries in series all the way down if you can. It's not always possible, but even if you're only getting dozens of charges out of a set, they should still be economical compared to alkalines.
The relatively abrupt voltage decline when NiMH are fully discharged might make this hard to manage if the remote doesn't turn on its battery indicator until the batteries are almost completely empty. You might be better off just charging your batteries on a schedule instead of waiting until the light comes on.
If that battery is bad enough to be a problem, I suppose you might as well go ahead and replace it, in which case, another battery will likely become the weak link. That's just the way it goes. You could also try doing a couple refresh cycles, especially if you have a fancy charger with that function built in. I'm not sure that does anything for NiMH batteries that have experienced reversal, though.