Shoot. Figured it out. It is a me being stupid problem. But I'll leave this up in case someone else does the same stupid thing.
What happened: I had one day where I had to update my slides from home, using a different computer. (It was 7 am, and I had just realized that I didn't have slides for my 8 am class.)
If you run pretext-deploy on a different machine, and then return to the one you usually use, tracking of the gh-pages branch gets messed up.
But it doesn't seem quite as simple as "Sean forgot to git pull when back in the office" because the source files on the main branch are up to date and have the changes I made from home.
I guess the moral of the story is that you shouldn't run pretext deploy from more than one machine.