You have compared a trace made with a very old HDTune (2.55) against the current V 4.60 which has lots of problems with certain types drives. I wouldnt touch it until next vers comes out. You need to run ATTO bench or HDTach 3.0.4 in XP SP3 compat mode
First of all the "degradation" prob is only on the Intel southbridge, so you need to be in AHCI or RAID mode to even be on the chip at all.
Secondly, the ASUS guys here have repeatedly said you need the latest drivers for everything
When installing Win 7 it will install generic MS 2006 AHCI drivers
In Win 7 X64 it does not accept latest inf on USB stick - it will install MS 2006 generic AHCI
You have to run the cd.exe AFTER install
Intel RST 10.1.0.1008
Chipset 9.6.1021
Intel MEI plus update
So you are scaring the crap out of the people here
Heres my HDTune on a WDC 1TB FEAX
Now there is a problem, whereby my burst is lower on the SATA 3GB/s ports than I would expect, and when I have time I will move my drives over to the Intel SATA 6GB/s ports and see what happens