Also make sure the 2 drives were not configured as a RAID 0/1 pair, because that would allow you to see only one drive. Many two bay Laptops allow this feature in the BIOS. Desktop PCs would require a RAID Controller Card.
One other thing you could try to test the second HDD would be to shutdown the PC and Boot of of only the Drive in question by removing the functional one. The BIOS would then tell you whether the drive is defective or not. Also, as previously mentioned, if the HDDs are IDE, check the Jumpers before testing the inoperative drive.