Basically the same issue with me.
I can put an SSD in slot 1 and another in slot 2. When I boot my machine (Windows 7 Ultimate x64), it only recognizes the drive in the first slot. I then shutdown the machine, swap the drives, but it still only recognizes the drive in slot 1.
Did anyone ever figure out how to get both drives recognized? I'm using an eSATA connection between the dock and the PC. Haven't even tried the USB connection because it would be so slow vs eSATA that it would be useless to me.