Check:
1. Is your 2nd hard drive's jumper set to slave?
2. Are all the power and hard drive cables properly connected?
3. Have you tried using your 2nd hard drive as the master? Does it work?
4. Have you tried using new cables instead?
5. Is your second hard drive old as in very very old?
Chances are it maybe a problem with your jumpers or cable connection. Or maybe your hard drive has lost its low level format which is necessary for the motherboard to read it.
Hope that helped