I would take a look at temps and voltages first using HWMonitor:
HDD temps should be below 40c and voltages shouldn't be straying far.
If that's looking good, consider adding a cheap ($15) PCI controller and running your drive(s) off that.
I had posted a message about this some months back and it was inconclusive at that point in time. I tried to post on the same thread, but it was inaccessible. At any rate, during certain HDD intensive tasks, my computer would lock up while my hard drive did a temporary rumble. This rumble is always preceded by a lower pitched (much quieter) sound that is similar to a pneumatic wrench that you would hear during car repairs. As this is happening, all activity on the computer freezes up. I mean, everything. I can do the same tasks on a computer with nearly the same specs and it doesn't happen, ever. In fact, it has never occurred on any computer I've ever owned. I even called HP and they had never heard of it--to the point that they thought I was lying and attempting to get free hardware. I had spoken to multiple personnel, including the usual techs to elevated supervisors, etc., so I finally gave up with HP. One new development has surfaced, however, and that is that the effects are lessened and minimized (rarely occurs, but still does sometimes) by a recent Intel Storage Manager driver update. I don't know how much a hint that is, but it may be a key in figuring all of this out. My guess is that HP included a faulty driver or motherboard and the update alleviated some of the symptoms of that. The motherboard is an Intel w/ICH9R RAID controller--not sure of the exact model. I had also replaced the original hard drive several times to rule that possibility out. So I am hoping some of this new info might help narrow things down or (hopefully) help a light "click" for someone.
Thanks in advance,