I've also had Reminder/Alarm/Notifications issues (though the innate alarm system works).
Wosto sent me his own fix which I'm sharing here. This might or might not fix your issue and you should handle with all due respect to the WM5 notification queue:
[WARNING: Do not manually delete notification events unless you are certain you know what you're deleting. If you delete events indiscriminately, you could lose the ability to use ActiveSync and you will need to do a hard reset to correct the problem!]
1. Get and install Scarybear's:
http://www.scarybearsoftware.com/checknotifications.zip
2. Run and "Clear" duplicates
3. Then check for resident notifications with a "NULL" value in the Dialog Title (The first instance of VCCalendarReminderShadow comes to mind).
4. Delete that value (click and hold). Reset and see if it cleared the problem. It cleared mine and I have repeating alarms/notifications now though I have not re-tried 3rd party software yet.