Hi Guys, remarkably, in 2015, I have the same problem. I have an early 2011 15" MBP, other than having an original Apple SSD in the primary slot and a 1TB mechanical drive in the optibay slot, my problem is the same as everyone elses here.
In the last couple of months Apple have recognised a problem with the 2011 series of MBPs and are testing and replacing LogicBoards under warranty, even if expired. This was manly due to poor soldering with something to do with the video card resulting in garbled screens and random reboots.
My MBP was largely fine over it's life, but started playing up more frequently about a month ago. I found out about the replacement program and swapped out the 2nd HDD (and just left the slot blank) and took it in for warranty. Video card faulty and replaced. When I got it back, it was just the same and I never even bothered putting the HDD back. I took it straight back, they confirmed the new LB was also cactus and again replaced it under warranty.
I've had it back about a week now, and it's been fine. I went to install the HDD last night and just run into problem after problem.
Prior to taking the laptop in, I wiped the 2nd drive, and made an image of the SSD. I had the image saved to the 2nd drive. I then reformatted the SSD with Yosemite, complete fresh install. I even mounted the image (prior to installing Yosemite and then again after) and the image was fine. I'd created two partitions on the 2nd drive (I don't know why) and removed it.
When I reinstalled it, I couldn't read the image. I could eventually get it mounted, but when I tried to read something or copy it out, it would crash. A complete system crash and go into a reboot cycle twice before coming back to normal.
Then the image was corrupted and I had to manually mount it. It crashed again, and again, and again.
I was slowly getting data off it, but the constant crashing was concerning me and prior to going to bed, I felt it HAD to be the LB. I did not think it was the drive, although Disk Utility was reporting errors on it and not loading it, but then it would, and then it would crash.
Today, I have put the 2nd drive into a Mac Mini and I am in the process of copying out all the data without a problem. Slowly getting it all onto an external drive over USB2 :( But at least it's working! :D
Because of the crashing, I'm more inclined to believe it's the LB, but after reading these posts, I think I'll grab the connector first. I am yet to reinstall the superdrive and give it a go (I'm not too sure where it is).