Update:
Before I powered up the system this morning I swapped my HDD into sATA port 2 where my DVD is and dropped my DVD down to sATA port 3. Again, the DVD was detected properly and the HDD was still not showing up in port 2. I powered down the system and swapped them back to where they were and the bios saw the HDD as it should (I am posting this update from the system in question).
Still pretty stumped, although I should be able to get my hands on a friends system tomorrow to try it in. We’ll see what happens.
