As I did not write any of the scripts used to run this site, all of this is pure speculation, albeit from someone with a bit of background in dynamic web programming.
You may have also noticed that the board runs slowly at times, and that there has been a recent recurrence of Oops! messages, though not all the time, thank Jeebux. What this means is that the database is once again getting too big, ergo the server is once again getting overloaded, and we are soon due for another archiving.
This relates to the original question because programs often include mechanisms to discard inessential functions when having trouble executing essential functions. In this case, essential functions would include user login and basic display of messages, while alerting of new posts and jumping to the newest post in a thread (all custom features by Evan, mind you ) would be pleasant but inessential features rather than necessities, and would be the first to go when the wheels are having trouble executing their basic rotation.
One thing that may be contributing to this is things like wasting space.
I'll note that even if the database size is not the cause of the wonkiness of the "new messages" features, it still is, as always, a brilliant idea to try not to waste space on the board.
I can't keep my fingers out of any pies!