I've had essentially the same problem when I've tried putting in a lot of new entities. I was working with the Civilization Forge mod and then tried to change ethics so that my civilization both worshiped and was friends with Pedobears and Cockmonglers, only to find that out of the blue the entity I wanted to play as would never actually exist even though during worldgen it would specifically say "Anonymous Town XYZ." It kept switching to High Elves, then Cave Crocodiles, kind of like the OP's problem. Long story short I had to start with the last copy of DF before the buggered up one. Really, the lesson here is to always save your modded games once you know they're stable before you start modding the crap out of them again.
My theory is that it has something to do with all those repeated generations of screwed-up Elf-dominated worlds (Once I got an Age of Anonymous that actually meant that the Elves were the main power. At that point I basically stuck in [INDIV_CONTROLLABLE] on Anons, killed every elf I could find, then switched to a different game copy), it probably changed something in the data file (other than the saves file, of course), which pretty much means you're screwed as far as modding goes. Oh well, as far as I'm concerned it just makes the whole thing more fun.