An admin of this xenforo site says that certain threads don't show up in the What's New? section and that they can't merge them? What sort of issues would cause that problem? Their board did not start on a new board but was an import from vBulletin.
Threads don't show up in What's New if they do not contain unread posts. They might be interested in this: http://xenforo.com/community/threads/add-latest-threads-to-navbar.8502/ An inability to merge would be a lack of moderator permissions.
Most likely they've hit the performance issue with merging large threads. One of those is 29,000+ posts in size. In my experience thread-altering operations will fail/timeout on a thread of that size. Listed as a Future Fix - http://xenforo.com/community/threads/thread-merging.18717/
