In my experience, the display of New Subscribed Threads (on the UserCP, Lou) has been acting strange lately, but I can't pin down the problem. Since I check in to the forums from at least two different computers and from my Android phone, I think the timing is getting screwed up somewhere.
To resolve the problem, I click on the List Subscriptions link under Your Control Panel / Subscribed Threads on the left side of the UserCP screen. That list is sorted by date of last post for each of your subscribed threads.