I hate when these type of things happen involving the whole chkdisk utility, as it never does any good. The thing is if you cannot do a system restore, just about the only other option available besides a complete format would be to run a start up repair. If you have the DVD, boot from it and select the correct option when you get into it. You may be able to run a system restore from there as well. If those options are a no go, I'm afraid that you may be forced into doing a clean install. But give those options a try first.