I can only assume that my experiences in the old days of '95 still hold true. In some cases, a single Windows file can become corrupt but, because its there, when Windows insta;lls over the top, its not changed. And, of course, no-one knows what file this is. Under these circumstances, the only thing is to ensure that you have all your important files, wipe you c;| drive and re-install.
If you've got a Parition Manager, I suggest you store the old system somewhere futher done you HD just in case - but make sure that your nrew installation goes onto C:\ - not over your old copy.