Make sure that they are not READ ONLY files, after a restore from SPB back up all my files were read only and it was driving me crazy. If there is a program that is running at start up and will not allow you to delete it because its in use, you can use
SafeMode for PocketPC. This may not apply to you but I've had to use it a lot
Edit. I thought this was a file and not a reg key, Although I can't find the reg path. You may try
MemMaid or
SKTools to clean the notification que.