I have the same problem. I used OptiBay knock off. I have the Vertex 3 SSD in the standard slot and original 750 GB HDD in the optibay.
At first the I could only see the HDD drive in Disk Utility, but I could not format it. However, it worked fine when I put it back to its original slot.
Now I figured the optibay is just broken and put everything back, Superdrive and all, but the eject button doesn't work and the whole Superdrive is gone from the system profiler. So, Superdrive has power and hums sometimes, but it's not visible to the OSX.
I can see that I broke a little bit of the optical flex cable so I'll order a cable and see what happens.
I feel like an idiot now. Why god, why?
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UPDATE (22 FEB 2013)
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1. closely examine have you damaged the superdrive cable. If you see a small tear in cable, it's probably it.
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2. Buy a new one (choose one that is correct for your mac, there were more than one..)
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Mine (Late 2011 MB Pro) was fixed with a new 30 dollar "Optical Drive Superdrive Cable for MacBook Pro 15" Unibody"
I have the same problem. I used OptiBay knock off. I have the Vertex 3 SSD in the standard slot and original 750 GB HDD in the optibay.
At first the I could only see the HDD drive in Disk Utility, but I could not format it. However, it worked fine when I put it back to its original slot.
Now I figured the optibay is just broken and put everything back, Superdrive and all, but the eject button doesn't work and the whole Superdrive is gone from the system profiler. So, Superdrive has power and hums sometimes, but it's not visible to the OSX.
I can see that I broke a little bit of the optical flex cable so I'll order a cable and see what happens.
I feel like an idiot now. Why god, why?