Windows 7 Freezes And Is Corrupt?

A few weeks ago my computer started acting strange, in that mozilla firefox would freeze a few seconds after I started it. It would usually unfreeze about 10 seconds later, but sometimes it never would and I'd have to restart. I figured I could live with this until last week when the problem got worse and the freezing would last longer (and more often be permanent) and it didn't always require opening of the browser to trigger it anymore.Last week I re-installed windows 7 on a formatted partition, but the problem quickly came back. In fact today it was worse than it's ever been - my computer froze so I had to hold the power button to restart it. After that, I couldn't even start windows without it just hanging on on the loading windows page. I ran windows repair multiple times and kept being told that windows repair couldn't fix the problem. I tried running sfc \scannow but the computer wouldn't let me because it kept saying it had a pending repair and I couldn't get rid of the pending process. Anyway, I re-formatted the partition then re-installed Windows just now, but figure this problem won't go away unless I get to the bottom of it. Obviously a re-install isn't the answer since it didn't work the first time.For full disclosure - I have a 2nd partition and a 2nd hard drive installed on the computer that I did not format when I re-installed windows either time. One is work / program files, while the other is photos and videos. Obviously I can't just delete these, and if I back them up and restore them, any trojan or hijacker hiding in them will just return.Could this be a hardware issue, or does it sound like there's something more malicious here?At this point I've only installed Avast anti-virus and the windows updates. Please let me know if I should run any scans and post back here, as I'd really like to get this issue fixed ASAP so I can use the computer productively again.