I just posted a thread a few pages back (
http://forum.ppcgeeks.com/showthread.php?t=17518) asking about basically the same problem.. I'm wondering if HTC has anything to say about it if I were to call their Tech Support. I have a feeling they'd say they have no idea because they don't support WM6. But it's really making me mad that it does this, as email and txt is my main method of communication. Thinking about returning it for a BB Pearl. I don't like having to soft-set the phone 5+ times a day to keep my notifications working.
Edit: Also should say to the threadstarter; I don't think it has anythign to do with your applications you have installed.. Completely stock my phone started doing it to me after having it for approximately a week and a half..