Processes And Applications Freezing - Disk Needs To Be Checked For Consistency

I run a windows 7 7600 build, which is not genuine. About two weeks ago, nearly every time I booted my computer, iId get "one of your disks needs to be checked for consistency" message, while windows would carry on with the said process, isolating, replacing and deleting all files necessary. I run a full scan, with my avg, found no virus, did some more scans, and the said process has stopped occuring. However, since this has stopped, my computer has been consistently and very much frequently been freezing processes and applications for a period of 2-20 seconds.

Games would freeze on their tracks (especially frustrating on the online short) photoshop brushes would stop rendering, movies would stop their videos (oddly sometimes the sound carries on), internet explorers would stop loading etc. etc. I've defragmented my 0% fragmented drives, just in case, yet the problem persists. I saw somewhere that windows might be pulling this trick, so i'd get the genuine ones. but i can't imagine that's the case, because windows have detected my version as not genuine for a couple of months now, (run as genuine for about half a year before).