Put the SSD in where the internal SATA HDD used to be and it's been booting without issue ever since.
There is a known issue with SATA III and the optical bay on 2011 15 and 17 inch Macbook Pros.
My guess is Apple didn't fix the issue for 2012 seeing as the large majority of users do not replace their optical drives with an optical bay. It also voids the warranty.