I have the same problem, I'm using XP Pro Version 2002 SP3, with .NET 4.0 (I tested the versions 3.0, 3.1 and 3.5)!
Does anyone have some idea?
From what I know, .NET Framework has nothing to do with the double folders. They are created from the multiple installs of SolidWorks. Personally, I would uninstall all of the versions from your PC, clean the registry of SolidWorks registry keys. If you search the forums there are plenty of examples on how to do this and reinstall fresh. This should restore all of the links to .NET and other MS redistribuitables.