Why do you have to OS's?
And If you reformat you will lose everything that includes system files as well as personnel files.
When you reformat and you put the OS CD in and install it the problem would be solved but I wouldn't do this as a first option.
What protection do you have? (Like AVG, Superantiwpyware,...)
Do you have the disk of the OS?
Do both OSs have that same problem?
If you have the disk you can try start -> run -> type "SFC /SCANNOW"
This will check if all windows files are there and will renew them if lost.
You can also try start -> run -> type "CHKDSK /X /F"
Here you will not need the CD but I don't really think that this will fix the problem.
There are still some other ways to solve this problem but first I need an answer at those questions.
Jonas