Does the new machine have a new SATA drive?, if so, is it SATA 3?, if both are true, make sure your SATA cables are also SATA 3, I had similar problems when I upgraded my drives from SATA 2 to SATA 3 and used the old cables, sometimes it would see all the drives, sometimes it wouldn't.
After swapping the SATA cables to SATA 3 ones, no further issues.
Admittedly, it could have just been a bad cable, as I know SATA 2 and 3 are compatible, all I know is, I was having some really weird issues until I bought new cables, and have not had a one since.
Steely