hmm. There could be a few reasons for this.
1. loose power cable for the hard drive
2. loose data cable for the hard drive
3 Hard drive is going bad
4. Could be a motherboard problem
A. Check all cables and reseat the ones pertaining to that hard drive (both ends of the data cable)
B. If no change after using system for a while, test hard drive, some boards have a hard drive tester built-in to the bios or to the F12 boot options.
Well since I needed to use one of the Harddrive I decided to reboot, and it still didn't show up. But then I rebooted again and checked the BIOS. Both harddrives showed and when I finished booting the Harddrive is now showing up. So it appears rebooting doesn't fix it but opening the BIOS does, but after time it doesn't show up again.
I would still check all of the cables as that is common and reseat them also.
I would do the hard drive test also.
Windows may be having a hard time loading the drivers for the hard drives because the hard drive could be bad or any of the other reasons mentioned above.
I've checked all the cables, what do you mean by "reseating" them? Also I think it becomes "inactive" when stopping or starting a Frap recording. (Doesn't do it the first time I try, but maybe Fraps writing onto it is a cause?)