Okay it seems like some models of MacBook Pro have issues with a fast (6Gbit/s) SSD in the optical bay. Even though my Mac says it offers 6Gbit on both bays it simply didn't work in the optical bay. So I switched places between the two drives and everything seems to work. My Mac booted from the old HDD in optical bay automatically and then I cloned it afterwards and changed the startup disk to the new one. As said before, don't put a fast SSD in the optical bay!
I've replaced the optibay with a samsung 840 pro but can't format it nor copy files (a few files work) to it. Do you suggest putting the HDD in the optibay instead? Did you clone the HDD to the SSD before swapping them? Will my Mac boot from the HDD the first time I boot even though it's in the optibay? I would really appreciate an answer, I've spent too many hours trying to figure it out!