It's possible the drive is failing, very low performance is often a symptom. Of course, you don't want to hear that but with a modern system like yours, low HDD performance isn't usually a systemic issue, though switching to PIO was an interesting technique.
Did you use chkdsk with the /r switch to run a surface scan? /f or no switch checks critical file system structures, but won't find issues from the hardware.
Of course, perhaps I'm a bit biased- I had the EXACT same drive in my own system, barely used, as a third hard drive, just last week, and it started giving me similarly bad performance- I replaced it thinking i was being picky, but now the drive is nearly unusable when I tried to transplant it to another system, disappearing from the system, no longer surviving a basic checkdisk as it did at the time, fails the seatools short and long tests, etc. seems it barely survived the cloning process at all!
Best suggestion would be to run the bootable CD of Seagate's Seatools. You can at least fully verify that the drive has no bad blocks with the long test, but make sure to set aside a good number of hours to let it do so. I'd go so far as to say to even replace it before doing so, simply because the act of checking the disk may itself exacerbate the issue and turn it from a low-performance issue to a salvage operation, as I discovered with that very model.
