Original Apple HD has issues in optical bay with OWC Data Doubler

I have had this hardware setup for about a year and a half now with no issues and have not changed anything hardware-wise since. This problem started when waking my machine from sleep last week. I have a Mid 2010 15" MacBook Pro, upgraded to 8GB RAM and I removed the superdrive, moved the original Apple hard drive to the optical bay and put a Crucial M4 SSD into the regular hard drive bay.

The SSD is my main drive, the original Apple drive is just extra storage for files and things which are temporary, or don't need to be backed up.

A week ago, I put my machine to sleep by closing the lid as normal. When I woke it from sleep by opening the lid (same as always), I got an error that my second hard drive had been ejected improperly. After that I could not remount it. Disk utility (gui and command line) didn't see it, it didn't come up upon reboot. I have done the following troubleshooting steps trying to cover both hardware and software:

- Removed the drive and put it in an external case. The drive functions just fine.

- Put the Superdrive back in the machine, the super drive functions just fine.

- Replaced the OWC Data Doubler, this hasn't fixed the problem

- Reset the PRAM

- Reset the SMC

- Run Apple Hardware Test, short and extended tests, both came back with no trouble found

- Installed Mavericks on a different external drive, booted from the drive. It sitll didn't see the secondary hard drive

- System Information (formerly System Profiler) does see the secondary SATA chipset but shows nothing attached to it

- checked for current SMC and EFI updates (I appear to be current)

- checked dmesg to find many of these messages, that I'm not sure are related:

SMC::smcReadKeyAction ERROR IN1R kSMCBadArgumentError(0x89) fKeyHashTable=0x0xffffff801ba0f000

SMC::smcReadKeyAction ERROR TB3T kSMCBadArgumentError(0x89) fKeyHashTable=0x0xffffff801ba0f000

SMC::smcReadKeyAction ERROR TG0H kSMCBadArgumentError(0x89) fKeyHashTable=0x0xffffff801ba0f000

SMC::smcReadKeyAction ERROR TG1H kSMCBadArgumentError(0x89) fKeyHashTable=0x0xffffff801ba0f000

SMC::smcReadKeyAction ERROR TN0P kSMCBadArgumentError(0x89) fKeyHashTable=0x0xffffff801ba0f000

I read sometimes these can be caused by a bug in iStat. I don't run it, but I run iStat Menus, so I updated that. That didn't fix it.

I've read about the 3gig vs 6gig SATA drive issues with the data doubler and the optical drive bay. That doesn't apply here, I'm using my Apple original hard drive, not a 6gig SSD in the optical bay.

I seem to have ruled out as much of the hardware as possible - drive works independently, connector cable works with super drive, logic board onnection works with super drive, OWC data double has been replaced. I don't think I can update firmware on a Apple ROM'd hard drive.

I seem to have ruled out software - clean install of maverick on a external boot drive, reset SMC, reset PRAM. I may try booting to an external drive with 10.7 or 10.8 to see if that makes a difference. It didn't change after any kind of update or software install.

What am I missing? Anyone run into this issue before? I'm an experienced HW and SW troubleshooter and it seems like I've tried all the most obvious break points. Any help or suggestions would be greatly appreciated.