Just noticed that when I use the code from the Codex to exclude a category from my index page, the index page displays fewer posts.
For example, I have 5 posts per page set in Admin. I just posted five posts to the category I'm excluding, and my index page is now blank! (Imagine how I freaked out before I figured out what's happening!)
If I set my posts per page higher, I then start seeing my earlier posts in other categories. The easy answer is to set posts per page very high, but this will make my archive pages and RSS feeds very long (curiously, the feeds aren't affected, which might be a clue to how I can fix the index page).