I checked again this morning and it's no longer showing in BIOS on boot. Could it possibly be a bad board on the drive itself? Would this throw any errors in Windows?
I thought that I would try transfering some files to and from the device last night. Speeds from the device were in the 28-33 MB/s range, but when i transfered to the device it fluctuated from 1 KB/s to 34 MB/s.
I also forgot to mention that it clicks when spinning up from a cold boot and sometimes clicks when running, and it won't read/write while clicking. I keep thinking it's a bad drive but as I said before it pulls up fine when I rescan once its through clicking and it has passed every test I've thrown at it.
If not, do a full Error Scan on the Error Tab with HD Tune (Pro).
Also, do you have a spare SATA drive (nothing needs be on it) that you could plug into an adjacent SATA port from the same controller in addition to this drive, to see if the MB BIOS recognizes it properly when you don't see this drive?