I had an exact same problem about 6-7 months ago. Little "You have received a new message from..." pop-up notifier suddenly stopped appearing. Whatsmore, when you open Messenger Window, the "No new messages" sign was not getting updated. I would exit the Messenger, sign in again, and then it would say "1 New Message". When I click, and view the message, that Messenger window does not get updated, so it still used to say "1 New Message". Only after closing/signing in again, it would say "No new messages".
I tried it at work, at home, and from a friend, with Messenger 6.2, and two other previous versions going back to v4, from three different PCs. Removed/reinstalled countless times. Then I signed in with my other hotmail address - and pop-ups were working! Signed back in with my usual name, but nothing.
Posted an issue here, I found other 5-6 people who had the same problem, but the majority is just fine. When I saw this message, I immediately tested it, but it works fine for me now. My guess is that they're upgrading your Hotmail Inbox to 250 Mb, because 2-3 weeks after the problem disappeared for me, I got a larger Inbox, and this somehow messes up the new mail notifier. In any case, I think it's a problem with MSN internet service, absolutely nothing to do with your PC. What I did though, is send 2-3 bug reports to Microsoft, from
http://uk.support.msn.com/contactus_...c t=eformfree
After several automated replies, I was finally getting some feedback from developers, however, make sure that you specify when you write to them that it is MSN MESSENGER, not MSN EXPLORER that you run. No matter how many billion times I used to write this to them, I would always get an email from some other guy at Microsoft, asking me for MSN Explorer log.
Anyway, the problem "fixed itself" in about 2-3 weeks time, but there's no harm in sending them few bug reports.