Well, I've got a new problem now. My math fonts for LaTeX are all kinds of screwed up, as described here and many other places. Sometimes if I view a PDF with LaTeX generated equations in it in Preview everything looks fine, but if I just change focus away from Preview and go back it could get screwed up. Here's a video of what happens:
Googling told me I should try wiping out ATS databases with the following commands:
atsutil databases -removeUser
sudo atsutil databases -remove
(Gotta log out after running just the removeUser option, and reboot if you do the full on remove as root). This seems to provide temporary reprieve, but I start experiencing font breakage again after not too long of messing around with generating PDFs from LaTeX.
So annoying! I really hope this is just a display bug and my PDFs are actually fine when I email them to people or print them. It would be nice if this somehow gets fixed soon.
Update: I reinstalled Leopard, creating a new home directory and everything from scratch, and this problem magically disappeared. Go figure.