"I'm having nearly the exact same issue. My logic board suffered some unfortunate liquid damage earlier this year (MBP wouldn't even boot). I found a guy on ebay who does logicboard repairs rather than replacements (saved me hundreds) and my computer worked fine for a couple months. I recently replaced the SuperDrive with a Kingston SSD and everything was working fine for a few weeks.
One day when I got home from work I got a kernel panic and my computer refused to boot. I reinstalled SL onto the 320GB HDD that came with the computer via firewire and Target Disk mode (I had converted it to a storage drive) but was unable to write to the SSD. I was able to recover data from the drive using DiskWarrior, but I could not write, erase or repartition the SSD. I tried to repair the SSD using Disk Utility several times, each time with ""success"" but I could not use the drive. After a day or two, the SSD stopped being recognized by the computer (not showing up in Disk Utility or System Profiler).
I removed the SSD from my MBP and put it into my hackintosh where it functioned normally. This obviously rules out drive failure. So I put the SuperDrive back into my MBP to test the SATA connection, and it too fails to be recognized by Disk Utility or System Profiler.
Now I am having the exact same issue as you. There is a problem with either my Super Drive cable (flex cable?) or my logic board itself. Since I've already had issues with this logic board (and that was the cause of your problem as well) it seems only reasonable that it's the culprit in my situation as well. Perhaps an important difference is that my computer continues to function normally when booted from the other internal drive regardless of whether the SSD is connected.
I think maybe I just melted a solder or something (or with a huge amount of luck, I just need to replace a cable). What are the odds of being able to repair my MBP without a full logic board replacement? It's already out of warranty (which was surely voided when the logic board was repaired the first time anyway).
I could probably send my computer back to the guy that fixed it the first time, but that cost several hundred dollars and shipping to Canada ain't cheap. I guess I technically don't NEED the other SATA port, but SSD's large enough to replace both drives are too expensive for my recent-college-graduate budget. :-(
"Eerily similar problem here. Identical setup to the OP, except an older MB.
I have a Mid-2009 15""MBP. Swapped the optical drive for an OCZ Vertex 2 SSD and Optibay Knockoff two days ago. Worked great for about 12 hours before the system crashed and the computer became un-bootable.
-Took the system back apart, and nudged, unplugged, and plugged cables for a while to try to isolate the problem. Seems to be a physical problem - it would occasionally boot after disconnecting and reconnecting... but a tiny nudge would screw the whole thing up. I'm fairly sure the problem is where the logic board connects to the optical drive cable.
-SSD is still working in an enclosure. No such luck for the Optical Drive, which is now back in its proper place. It seeks on boot but isn't recognized by the OS. Yikes! Hoping the problem is with the cable, but like the OP I'm not terribly optimistic.
-Will be taking it to the Apple store soon... would rather not drop $30 on the cable if it's not necessarily the problem.
-Weird to have the same problem with the same SSD. Hope it's a coincidence...
Steven, what knockoff OptiBay are you using? Mine is the Nimitz model, available on ebay.
-Apple store and stomaching the logic board replacement if necessary is all I can think of now. Worth noting that this would be the second time the logic board has failed. Last time it was the actual HDD bay.
Anyone have other suggestions to test or repair it?
I have this exact same issue with a mid 2009 MacBook Pro. I'm using an OWC data doubler. I think it's the data cable, but it sounds like it's actually a problem with the connector on the logic board. It probably becomes damaged when disconnected the first time. Oh well, I'm just going to get a mobile enclosure for my HD and deal with it for a year till I get a new machine.
"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?
UPDATE (22 FEB 2013)
1. closely examine have you damaged the superdrive cable. If you see a small tear in cable, it's probably it.
2. Buy a new one (choose one that is correct for your mac, there were more than one..)
Mine (Late 2011 MB Pro) was fixed with a new 30 dollar ""Optical Drive Superdrive Cable for MacBook Pro 15"" Unibody""
