Alright, I got the fan working, but it only works when it's plugged into the SYSFAN2 slot, so I can only have one of my two case fans running. Basically, the SYSFAN1 slot doesn't seem to work. I tried connecting my other case fan (not the one I just got working) into the SYSFAN1 slot and it didn't work, so it must be a problem with the motherboard or something. As for the BIOS, there isn't an option for disabling any of the fans, or at least there isn't one that I know of.
My motherboard is the MSI G31TM-P21.
You know what? Nevermind, I'm not going to even bother. That server fan is just so loud. It's not worth it.