Since I cannot find any good references on Paragon's site, I browsed around the net a bit. It seems that you are not the only one with such an issue:
http://www.wilderssecurity.com/archive/index.php/t-309876.html
http://www.wilderssecurity.com/showthread.php?t=309022
What I get out of all of that is that the GPT Loader cannot see drives behind an AHCI / RAID / SCSI controller. If that's the case, IDE mode may be your only option. Under IDE mode, you will run into alignment issues on the 3TB HDD since it's an Advanced Format (4K / 512e) HDD.