Macbook pro will no longer boot from main sata bay after Yosemite

Hi!
I am really stuck as to why my macbook pro will no boot from the main Sata bay.
I have the macbook pro late 2011  - a few months ago I installed a samsung 840 evo, and moved the 500gb hdd into the optical bay and all has been working perfectly until last night.
I installed yosemite two days ago and it worked perfectly to begin with... then when I re opened my laptop everything was frozen. I restarted it and it wouldnt get past the grey screen. Then I managed to get it to the internet recovery stage....however it would not recognise the SSD, so I had to install Lion on the HDD.
After I logged on it gave me the message saying that the disc is not readable and on disk utility I can only see the "samsung ssd"  but no details about it.
I thought that the SSD may have gone, but when i removed it and plugged it in via USB I was able to boot from it with no issues.
Does anyone know if this has anything to do with the new OS? or whether it is the Sata cable?
Thanks for any help!!!

Hi, I have been having the exact same problem with a late 2011 MBP 15 inch. I replaced the hard drive with a samsung SSD 1.5 years ago, along with a samsung SSD in the optical drive. It worked great until the Yosemite upgrade. The MBP seemed to work reasonably well for a few days after the upgrade, but then it started stalling on various programs (spinning beach ball on Mail, Safari, etc). Start-ups were also longer and had a loading bar each time, which was new since the upgrade. I left the MBP to sleep last night and when opening it, it crashed and tried to restart. On restart it loads to the login screen, then after I enter the password it partially loads (based on the loading bar), then shuts off. I removed the SSD and plugged it in with a USG, but that didn't change anything. Here is a picture after using CMD-V before it shuts off.

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