I'm using the 1016 Drivers from Intel, downloaded 3 days ago so they are up to date.
The Disks are:
System: Western Digital Green 1 TB (3 Months old) 16 MB Cache SATA2
Extra: Western Digital Blue 500GB (8 Days old) 16 MB Cache SATA2
P31-DS3L Uses the Intel ICH7 SB and thus does not have ACHI so I'm using the Enhanced mode as has been suggested.
In Linux and OSX which i have installed on the computer there are no multitasking problems and the disk transfer speeds are much higher. So I'd say that this is a windows problem more than a hardware problem.