This post is long overdue, but since the question keeps popping up on various SharePoint discussion lists, I figured I'd document the answer here (next time I can just post a link instead of typing the whole thing out again).
Monday morning, the calls started. For some reason, long-time users were unable to edit list items. I figured we had a permissions issue, so I popped in to look at the Site Settings -- and found that I couldn't. A quick trip to Central Administration showed that I was still listed as a Site Collection Administrator, but I had no power at all on the site collection in question.