I juumped the gun, the other one was 7% finished.
It hasn't scanned the whole drive yet?
That's why you may not have seen the files on your other partitions.
No, it had finished scanning. I had tried to do a mirror image onto my external HD and it was 7% done when you said to shut it down.
After I had the problem with IE, I had to restart the computer. As soon as it came up, it has detected a bunch of virus's. This is what started this whole thing from the start. I couldn't get the virus's off and that is why I had to reinstall windows. Now it is doing the exact same thing.