Broken Hard Drive?

I restarted my computer and it ended up freezing at the BIOS screen because of my second hard drive, so I went into the BIOS menu and removed it, but when I auto detected'd it to put it in again, everything was fine but after saving and rebooting, there was no sign of the second hard drive in the hardware check during start up. Wtf?

Have you tried clearing the CMOS on your motherboard? Sometimes IDE autodetection can get screwed up and stop working, or only work sporadically. Clearing the CMOS can sometimes fix it, or if that fails, reflashing the motherboard BIOS. I've also seen this happen when the motherboard has been damaged (in at least one case after a known power surge).