I'm having the same problem. Mid-2009 MBP will not recognize the HD I added to the optical bay.
The SuperDrive was not functioning (would not read/write) for some time before I decided to get rid of it and instal an optibay.
I'm hoping it's a problem with the SATA connector cable or the optibay and not the logic board. The HD in the optibay works fine and the machine runs fine on its own. The only reason it might be the logic board is that I did have some water damage about a year ago and soon thereafter the SuperDrive started to fail. Could it be that the SuperDrive itself is fine and the logic board isn't communicating with it properly?
I'm going to replace the SATA connector cable and try and different optibay. Hope that solves the issue...