Hi Andrew.
I was having this issue as well. As with GamerChase, only the global Alfred keyboard shortcut remained at what I set, but themes, the clipboard keyboard shortcut and snippets were all reset. I don't use any syncing. It didn't happen on a new user account.
I fixed it by following your advice to GamerChase, but setting the sync folder to my normal preferences folder ("~/Library/Preferences"), where Alfred v2 had already saved some plists. This immediately solved the problem - all settings I had previously changed became what they were meant to be. It seems as though Alfred was saving the settings to that location, but then not reading them back from there.
