ahhh lol, yeah it depends how badly fragmented, and how much data it has to move. That shouldn't take long, but it might not fix the problem..... Actually it might take a while considering your problem. I can't think of any 1 thing that would cause a problem that bad.
Is your harddrive accessing the whole time everything is loading? Maybe if for some reason someone switched a setting in the bios to force like pio mode 0 or 1, but chances of that are slim.
Even if you did switch the harddrive I don't think it would change, you have a problem somewhere. Did you install the ide drivers that came with the motherboard, or an updated ide driver from the asus website?