After some headaches and much Google searching, Matt was able to find me some good posts to check; a couple threads suggested to uncheck 'Segment Scale Compensate' in every single joint. I was skeptical, saving the model beforehand with a new iteration number lest I screw something up royally (or if there were no effects shown) and have to revert.
This turned out to be what I needed to do. Why it's on by default, what it does... doesn't really concern me. I can look it up later.
I'm still working on texturing and I'm hoping to go with a higher-poly final result, but at least I'm no longer looking at a smashed, inverted lump when it's in the game world.