I recently had a similar situation that might pertain to your problem. I have a Gigabyte Z68 board that has 6 onboard (Intel) ports and 2 Marvel ports. My optical drive wouldn't be recognized for booting when plugged into the Intel ports because the Intel ports were set to ACHI mode due to wanting to gain the best speed from my SSD. The fix was to set the Marvel ports to IDE and plug the optical drive into one of them.