Startup folder doubling items

I'm on Windows 7. I think this may have been caused by me playing with the folders in AppData\Roaming\Microsoft\Windows\Start Menu\Programs and ProgramData\Microsoft\Windows\Start Menu\Programs. It's been this way for a few days, until I decided to check it out and see what was going on. Then I discovered (via Autoruns and Msconfig) anything I put in my Startup folder at AppData\Roaming\Microsoft\Windows\Start Menu\Programs is being loaded twice. Anything I put in the Startup folder at ProgramData\Microsoft\Windows\Start Menu\Programs isn't being loaded at all. I don't think it has to do with the registry, but I'm not sure. Can anyone help?
 
open msconfig and disable all the startup items and excluding wireless (if it is). You then need to delete the msconfig folder from registry and restart the computer. Now try to put those folders in startup.
 
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