Now that the paper has been handed in, I feel a bit better. It seems the strange things that happened to some of the files (corrections that didn't stick) had to do with some "rar" files that I had lying around, as backups for the dissertation. When these files were expanded by accident, they overwrote the existing files. Luckily this happened very late in the process of printing, but unfortunately I only realized what happened now.
So a few spelling mistakes in my appendices got through to the committee. And hopefully, post-defense, I can take a look at one of the printed copies to make sure that my "masters" here are correct before submitting a final copy to the school.
No big deal, really. But I guess I shouldn't have had those rar files hanging around, and for sure, the program shouldn't have overwritten the old files. That's just stupid.
So, really, it's the program's fault.
Anyway, everything's fine now.
Did I mention I'm done?