Do you see very high CPU usage when performing transfers to/from the HD?
I have almost exactly the same configuration (same motherboard and SSD, but with a Samsung F3 secondary) and my HD performs to expectations.
I did install the drivers from Intel: those on the ASUS site are v10.6.0.1002, whereas the ones I got from Intel were v188.8.131.522
However, I'd be surprised if that was the problem (though I'd suggest updated drivers for this and everything else on your motherboard if available).
You might try grabbing a disk diagnostic like HDTach and use that to see if anything obvious is out of whack (in HDTach the Info tab will tell you if your HD is using the right ATA protocol, and you can benchmark it to see how slow it is relative to review numbers)