I just discovered that this is an issue with comment pagination (in conjunction with using a static main page). In discussion settings, turn off the option to break comments into multiple pages and the problem goes away. A wordpress bug, evidently.
I’m having exactly this same problem – comments leading to a page not found due to the use of a static main page. Did anyone ever figure out a resolution?
thanks elanaspantry. I’m going to try search reloaded per your suggestion. These message boards seem kind of lonely when no one answers you, don’t they? still nice of you to post your findings re: searches.