OK I have run into a problem with the drive, well not directly.
I attached the new drive up and made a 500gb partition and a 1.5Tb one. Transfered all my information on to it no problem. I ran a few HD Tune benchmarks on all 3 drives (F3 500gb, Deskstar 1TB and the new Seagate 2GB). The F3 and DS1TB ran off the SATA3 connections like they have for months and the Seagate off a SATA2 connectin. The benchmarks ran fine, again no problems.
I then took out the DS1TB and replaced it with the 2TB Seagate. Attached it up and booted into windows. I ran the 2TB Seagate on HD Tune again and was met by very poor results. I ran it a few times, but it never got better. I then ran the F3 to have a look at again poor results. I thought ok then I will detatch the new drive and just run the F3 solo and run HD Tune. Again poor results. I think the images below will speak for themselves.
F3 before swap
Seagate before swap (Sata2)
F3 after swap with Seagate connected
Seagate after swap (Sata3)
F3 solo now
Obviously there is an issue here. Nothing in the BIOS has been changed, I have only done a physical swap over from the 1Tb to the 2Tb drive. Any idea what could have affected this?