NCQ is most likely the issue, it is not supported by many drives yet, and it [b]must[b] be supported by both the drive and mobo for it to be used. The increase in speed comes from the re-arranging of instructions to be excecuted in the fastest possible way.
Are both of your drives on the same channel? This can cause issues as only 1 drive is able to communicate with the mobo at a time, slowing down transfers and your mobo may be automatically compesating for this. Here is a good article on Native Queue Command
Could you post the model number of your mobo?