Supreme commander and Company of Heroes uses nearly 1GB of memory if you have it even more, World in Combat is quite bad, Crysis is even worse, if you have everything on the highest settings with AA and AF (which is do) things can quickly get out of hand in terms of memory use, especially with vista. Many games have bad memory leaking issues, Supreme Commander being the worst I have seen, though I wouldn't be surprised if the retail version of Crysis is worse.
Since this issue seems to have occurred from the start, did you by any chance have a card or onboard video card that had drivers on your computer before you installed this card? There may be some conflicting drivers.
I doubt believe the hard drive would cause this, while read/write performance does drop off as a hard drive fill up, video games are by far more reliant on the RAM, CPU, GPU and sound card then the hard drive.
James