I have a similar problem on EP35-DS3R and the F4 Bios does not help .
For me its a problem with the Board .
Running an installed Vista on IDE fine no problems and overclocks and no problems running Prime .
Install Vista with AHCI and problems develop later . Lost drive random BIOS freeze poor shutdown and deadly slow startup .Almost as if the controller cannot access/read the drives .Likewise my drives memory etc pass all tests .
Same drives ran as SATA 11 drives no problem on last non Gigabyte board .
Can find nothing on the web that will help in any way .
After four weeks of logging and testing i have gone back to IDE mode .