I have this issue peridically. To 'fix' I uncheck all the notification boxes, restart and check again, then restart for good measure even though they start working again before final restart.

I also have a somewhat similar issue that is tied to notifications, which pops up more often (weeklyj? I don't have mail notification light on (otherwise it blinks nonstop anyway), but the visual notifications stop when display is off. I.e. the pop-behinds aren't appearing so the top left six squares appear with no multi-window indication. To 'solve' I check the box for led notification, wait for next email to see it's working, then uncheck.

I've had these issues since day 3 or 4 and they still exist sfter a reflash so I know it's not related to anything I install, but there is an issue w/the 'system'.

I don't install much since not much excites me as 'must have' right now other than a few things I come across in testing and devels (like powatool yesterday). After playing with something(s) from those repos a day or three, I reflash to keep as close to 'out of the box' as possible. Most of what I install, even Nokia's 'blessed' Evernote (which is a dumb partial implementation that doesn't include what you need most: the note db!), cause one problem or another. That's why I carefully and methodically install something and reflash. Rinse, repeat.

IOW, I have had this same problem and know it isn't a particulary app/library.