Windows basically works from the registry, almost exclusively.
Files you can simply reinstall, this is any file; the registry however you must be careful about altering as it controls your entire system.
There are normally 4 Sections...
/Root/
/User/
/Machine/
/System/
Your settings will be stored on /User/ControlSet/
Anything is altered in there it will adversly affect your entire system. Particularly if it becomes corrupt.
The actual system <user>.pwl doesn't actually matter at all because it is rebuilt each time you login.
Your software is intern controlled via /User/Software/Microsoft/
There is a second set of this in /System/Software/Microsoft/
Knowing what settings to alter takes a good knowlage of Windows backbone.
as I said try downloading TweakXP, it should fixx things.
Registry Mechanic isn't free but again will fixx major problems.