I was told that I had to reformat my pc because I have corrupted files?

My pc is acting funny. It will not let me type some times, it will just shut off and say " Windows has recovered from a very serious ??? Something??? Anyway I purchased Spy doctor and it did find some infections and virus, but the program took care of it. I am now clean! However my Pc is still off on the deep end( giving problems) I called the company I purchased the program from and I sent samples of history files and malware detection files. I was told that I have no viruses but I do have corrupted files, and the only thing that would work from this point would be to reformat the Pc. I would rather find another solution to this problem.