Hmm, it just happened again without moving anything. The admin simply approved a comment in an existing thread in the mod queue. The post and thread show up under "latest posts" but no alert or bolding of the thread and subforum. Very frustrating.
EDIT:
Oh, I think I may have thought of a possible cause:
1. OP makes a thread.
2. User2 reacts to the thread and writes a comment that goes into the mod queue.
3. OP gets an alert for the reaction, clicks it, and visits the thread which resets some internal "mark thread as read date".
4. Moderator approves the comment replying to the thread.
Expected behavior would be for 4. to result in another alert, and the thread and subforum to bold. But possibly due to the way Xenforo is calculating "thread read" is causing this problem.