Macintosh bootable volumes are supported on the internal 2-port PCI card (part number TSATA) but are not supported on any of the other SATA cards at this time.
The Stardom RAIDSONIC ST3620-2S-S2 is not reliable when connected at 6Gb. It was designed for 3Gb SATA. If you connected previously using a 3Gb controller, even with 6Gb drives, the connection was 3Gb. With the 6Gb controllers and 6Gb drives, the connection is negotiated at 6Gb, but the connection is not reliable because of the older design of the Stardom chassis does not support 6Gb. The drives may not be recognized or if recognized, transfers will fail at some point.