If his sata controller on his mainboard, the logic board on his drive, or his sata cable are flaky, it could be increasing latency times on hard drive communications. It passed in Seatools for DOS, which indicates to me it's likely not bad blocks on the platter, but more likely latency issues communicating with the drive.
I'd recommend turning off all your startup items in msconfig, then doing a read scan with Victoria for Windows on the drive, making note of blocks that take a longer time to access, then repeat the scan and see if the problems always occur on the same blocks. This will tell you if the latency issue is being caused by a platter or non-platter issue.
Victoria will also give you all the SMART info on the drive with ratings on how dependable the specific field is. Lots of green dots is good. Few red dots is bad.
Could it be a heat related intermittent issue? Do you leave your computer on all the time? If so, shut it off when you start having problems, and let it cool down to room temperatures for an hour or so. Then turn it on and see if your problems have diminished or if they persist.
Edited by Gabrial, 25 September 2010 - 11:28 PM.