It's probably a quirk in the way the system works.
Without having recently looked at the code - I'm pretty sure it does a query on the database to find the most recent 10 or 20 posts and saves that information to the cache for a period so it doesn't have to keep doing new queries for every page view.
However, because the system doesn't know who is viewing the new posts - it finds new posts for all members, including moderators and administrators - and some of those threads are not visible to regular members.
Of course, before displaying the posts to a specific user, it will filter the list to only show those threads visible to that user - we don't want moderator threads showing to regular users.
Now, this morning (or this evening for some of you), the moderators had a whole bunch of threads being discussed in the moderator area (a lot more than usual) - so I'm guessing what's happened is that the list of new threads was dominated by moderator threads which you can't see - so you only get a couple of new posts showing up until enough regular threads get new content to push all the moderator threads far enough down the list.
So, if the system gets the 10 latest new threads (with the intention of displaying 5 of them) - but 7 of them are moderator threads - you'll only see 3 threads in the New Posts box.
At least I think that's what's happening.
