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I think I see what my problem might have been. When I downloaded the newest version of the game, I just dropped everything into the existing folder, replacing everything with the newer version (I wasn't sure where the saves were being stored, and didn't want to lose them). I deleted my game and did a clean download and it looks to be working as intended. 

Excellent, good to hear. Yeah, I definitely recommend copy-pasting the save folder rather than over-writing the game data; the latter should work in theory, but I wouldn't be surprised if it introduced some weird glitches if something went wrong in the copy or didn't match up quite right.