I also installed the latest WinPatrol version and then noticed items missing from my startup list in "System Configuration". I had a suspicion that it was due to the new WP version, and decided to do a system restore.
Now I see everyone else has the same issue.
I wonder if it corrupted anything else in addition to the startup items in the registry.
I guess I'll just be doing a system restore and stay content with the older stable version (In this case, the saying "If it's not broken don't fix it" comes to mind).