I've been wrapping my head around this problem for a while(check my other posts). I've been having some problems with a few viruses I got from a friend's hard-drive so I decided to do a clean install of the O/S and switch to the x86 version of windows 7 ultimate. I successfully installed it and the first thing I did after afterwards was to install the trial version of Kaspersky Pure Antivirus. Even before I got the new "collection" of malware my windows kept freezing during random moments (while playing games, copying files, even watching videos), for short periods of time (it was suddenly freezing with the HDD Load LED lightened up and after a while, 20 seconds or so ... it "started unfreezing" with shorter freeze periods. After I saw the same symptoms on the clean install I thought it was a memory or a hdd problem so I ran the windows memory diagnostic and put the HDDs through some scans and tests. The only problem i ran into was a warning message from the smart data the software HD Tune Pro got in the Health status: "Ultra DMA CRC Error Count" was "1". So, at one moment in the past i had a transfer error. It hadn't occurred again.
So, the issue is: I can't even run a full system scan on kaspersky without slowing down my computer to the pace I can barely open a .txt file. During a game installation I have to act like microsoft has switched back to singletasking.
Ask me for further details, because I think I lost track of things I tried in getting a proper diagnostic for my problem.