Alright, I put out a new beta already. @Hippyshake, I'm hoping it solves your error, so you should see results again. I think what happened in John's case is I stupidly made a last-ditch change to look up to the parent folder another level when looking for GOG game shortcuts, and didn't check to make sure that folder actually existed (heh). So I'm hoping that's fixed now.
Per Clive's issue, yeah, that's a completely separate issue. That one's more frustrating too, because I'm not sure there's anything I can do about it. From what I can tell though, it doesn't appear to be a typical situation. Still, I have no idea why Windows has his Start menu with those permissions. Does anyone else have Windows 7?
Let me know if you see any more errors. It's also helpful to list the games you have in your Start menu that are missing from the list, and games that show up that aren't games.
Thanks folks. :)