How or what did you use to clean things with?
Did you create a restore point before you started?
Have you tried a system restore to a point in time before you cleaned your folders?
Chances are you've messed up Windows 7's junction points.
You could try restoring your user folders, as explained in this tutorial. User Folders - Restore Default Location
If ever you do want extra drive space it's best just to delete the contents of your user folders rather than the folders themselves.
Your library structure is, if you will, a junction point for any folders in the library, regardless of where they are on your computer.
Once you break the links you experience problems such as yours.