I have exactly the same hardware, Mac Mini late 2012 and two Samsung 840 Pro SSDs and having problems too.
I got my SSDs installed fine and they're seen by Finder and Disk Utility but I can't use the other one. The system SSD works just fine but the other SSD can't be written to, because it causes errors all the time. Disk Utility shows that it produces a lot of UltraDMA CRC Errors whereas the system SSD has no errors at all.
Then I installed the original 1TB Apple disk as the other disk and it works just fine. So, SSD + HDD = works fine. SSD + SSD = Only one disk works.