You have six 3Gb/s ports. 4 native AMD ports and 2 Marvell ports.
Verify that your drive is connected to one of the AMD ports (SATA1).
Wow thanks Dereck! It seems I completely overlooked the simplest thing, I had it plugged into the AMD SATA2 port not 1. Puzzling to me how everything else worked fine but just write speeds were effected.
Here's a re run of ATTO