I have a mid-2012 MBP. I just replaced the superdrive with a Samsung Evo 840 1TB SSD. My mac will boot from this drive when it is in the primary bay, and also if it is connected externally with a USB3/SATA cable. However it will not boot from the optical drive bay.
Also, if I install my original drive (Seagate Momentus XT 750GB hybrid) in the optical drive bay it will not boot.
If however I install an old 5400 HDD in to the optical drive bay, it WILL boot.
All three of the above mentioned drives have the same cloned OS on them. When the hybrid or the SSD are installed in the optical drive bay I can see them in the system profiler; both read a negotiated link speed of 6g.
Am I missing something...?