Xenforo stores the number of replies to a conversation in the Master table. When this gets out of sync, you have this bug. There are a number of reasons the increment operation could decide not to take, and it is one of the more annoying requirements of offset-based pagination systems. If you've ever been on a forum where there was a persistent issue that someone had to make an extra post on the last page of a thread to get a new one to show - very similar bug.
I at least got them to acknowledge it so I can fix it through the admin interface now, rather than needing to do manual edits in the database. It takes awhile, so I'll probably run it again once a new set of complaints show up.