That's odd. Nothing has changed on the forum side. What kind of alerts? Have you changed browsers, cleared your cache, etc? Try changing all your settings, sign out, then sign back in and restore them - then try a different browser. Play around with it a little bit along these lines; if nothing still works, we'll have to get the tech guys to take a look. No straightforward answers here for this kind of thing, sorry. It can be maddening, I know!
Note if you view the site and your alerts but don't go to the threads themselves the software auto drops those threads from your alert list until you view those threads again. It's a somewhat annoying approach because it means if you drop in for a 5second view of the site you MUST view every alerted thread at that point otherwise anything said after thatp oint won't ping those threads for a further alert.
Must admit I much preferred the old system that just kept sending you a notification on site that content was posted even if you only glanced or didn't look at the thread for a long while.