Aha, that was it. the first key (HKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\Shell Folders\Startup) was set to c:\documents...\All Users\... instead of my username like all the other folders on that page. Also, oddly enough HKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\User Shell Folders\Startup was set to %ALLUSERSPROFILE% instead of %USERPROFILE% like the rest.

The Common Startup was set properly, thus leading to the contents of it being run twice. So I'm guessing when I deleted the startup folder in my personal profile, it did that on it's own.

Thanks for the tip, I'll have to remember to check there in the future for problems with the folders listed in those parts of the registry.