First you should double check your systems firmware. Here's the Apple T/N on how to check and update: About EFI and SMC firmware updates for Intel-based Mac computers. While this is not your main issue it does effect you when running Windows.
The main issue you are facing here is a known issue with the Intel Platform Controller Hub chip this series of systems use. The secondary SATA port (Optical drive) is not SATA III (6.0 Gb/s) but something slightly in-between SATA II (3.0 Gb/s) and SATA III. This is a result of the clocking the chip uses. You will need to install a fixed SATA II drive in the optical drive carrier. It makes no difference who's carrier you use as the carrier is just a signal passthrough device. Here's OWC Data Doubler info page on their unit. Scroll down to the bottom of the page and just under the Red note you will see this:
MacBook Pro 13" models: Apple does not support the use of 6Gb/s drives in the optical bay. While we have observed a high rate of success using SATA 3.0 6Gb/s drives in Apple 13" bays where 6Gb/s link is present, some systems may not operate properly with this setup. For guaranteed reliability/compatibility, we suggest 6Gb/s drives be used in the main drive bay only, and 3Gb/s hard drives or SSDs be used in the optical bay when a two-drive configuration is desired. We cannot guarantee proper or successful 6Gb/s drive operation in the Apple MacBook Pro 13" optical bay.
OK, So I can't use the SSD in the optical drive then can I put it back into the HD's location and then move the HD over to the optical carrier? NOPE!
Sadly, you have two issues: Apples HD drive is SATA III so it too will encounter issues (file corruption) if used in the carrier just like the SSD. The second issue here it only the HD SATA port has CrashGuard to protect the drive from bumps. This is a sensor on the logic board as well as the rubber mounts for the drive. Some 3rd party HD drives have onboard drive protection which you will want if you still want the HD in the carrier.
OK, what to do here trying to install a SSD drive? Your options are a bit limited here:
Finding a fixed SATA II SSD is almost imposable now as all being made with auto SATA speed sense technology which won't work here as the SATA port is 1/2 between SATA II & SATA III (which is why it works sometimes).
The other option is to go with a larger SSD so you don't need the HD for the deep storage (big bucks $$$).
The next option here is to go with a SSHD which is a HD with a deep SSD cache. Seagate makes a nice one Seagate Laptop SSHD. We have fitted over 200 MacBook Pro's with them to gain performance. While it is not a SSD it gets you quite far.
The last option here is going with a dual drive that only needs the single SATA port (HD port). Western Digital offers a Black2 drive which is exactly that! It allows you to setup either as a Fusion Drive set or as discreet drives. I've played around with one for a while and it works quite well. We had already locked in on the Seagate solution before WD offered Mac support with their drive. We might have gone that way if the drive handled the bumps our field guys give the systems.
So the bottom line here is forget the optical drive setup unless you get a fixed speed SATA II drive (HD or SSD). Instead go with either the Seagate SSHD or the Western Digital Black2 drive.
Update: Western Digital has withdrawn the Black2. Your only solution now is the Seagate SSHD or the released WD SSHD (which is a fixed SATA III drive).
Your Windows 7 issue is related to how BootCamp works. You need to setup the SSD as your boot drive and run BootCamp (and Windows) within it. But until you fix your drive issues you'll need to wait to get this working.
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