I've this problem with my N900 :
sometimes my N900 doesn't alert me for sms (and missed calls, probably IMs, ...) (nothing, no sound, no light, nothing happens in the phone, BUT, if I myself open that person's conversation, the sms will be there), but when I restart it, it shows that I have for example 3 SMSs and 1 missed call and works fine after restart for some time!
I've upgraded it to 1.2 and I've installed a LOT of applications.
so, what's the problem?
what should I do?