WDC_WD1002FAEX-00Y9A0 not showing 6.0 Gb/s speed on MSI P55-GD85 Sata 6 controller

Check if the hard drive has a jumper on pins 5/6, that will also downgrade the speed. Also check if the link below helps.

http://community.wdc.com/t5/Desktop-Portable-Drives/1TB-FAEX-reporting-incorrect-SATA-speed-and-slow/td-p/109184

Jumper settings

http://wdc.custhelp.com/app/answers/detail/search/1/a_id/5387#jumper