Hi lllaass,
Here are answers to your questions.
How was OSX installed on the Samsung drive? I used SuperDuper. That's always worked for me.
If you reconnect the drive after booting from the internal drive does System Preferences>Startup Disk show the external drive as a startup disk? Yes, I can also see the drive when booting up holding the Option key.
Have you tried moving the Samsung disk to another bay? No, this is the next step. But I did try another enclosure and it still wouldn't boot.
Are there other drives in the enclosure? Yes, the enclosure holds 4 drives.
Does the Samsung drive have the latest firmware? I tried looking for the latest firmware, but cab't find it anywhere.
Notice the two pictures. The folders in the internal drive are correct. When I SuperDuper'd the internal to the external drive, the external drive looked identical, but after I tried to use the external as a boot up drive, it created extra folders which you can see in the pic below.
I don't know how to proceed. Maybe it's just a firmware issue, but I can't seem to locate that. Thanks!