?? The card you linked has a 4 pin fan connector, all 4 leads used - Blue, green, yellow & black. 'Tho there's a slight risk, what I'd do is flash the bios from another 9800GT, IF you have a spare PCI video card so that if it doesn't work at all w/new bios, you still have a way to boot to a DOS prompt to reflash the original bios... meaning you'll need to backup that orig. bios first. You might also post the orig. bios somewhere, maybe someone will see something if they take a look at it.
If the fan does only have 3 wires that could also explain it, 4th wire being for PWM speed control. It's possible to change fan speeds without it (generally speaking, electronically), but when a util uses a % method it's usually through the PWM change of the 4th wire.