Yes the NIC's are setup for Gg Full duplex- using auto neg on both cards (all 6 ports) and Brocade Fastiron Super X switch.
I have also disabled in Windows all NIC's before adding Hyper-V and then rebooting and reenabled 1 NIC - same result.
We do have Four other Win2008 R2 servers running Hyper-V fine - these are an older gen Intel Server
These older gen boards are - BIOS Version/Date Intel Corporation S5000.86B.12.00.0098.062320091136, 23/06/2009
I have taken our 16GB of RAM - this leaves 32GB in the system. By doing this it appears to have doubled the network throughput.
This is still under half of the throughput when Hyper-V has been removed though.
As we are a Intel Premier Channel Partner we will also continue to push our contacts at Intel to see if this is what is happerning with this board.
We also have a case open with Microsoft - so I will post the finds to this issue when we get to the bottom of it.
Thanks for your help here.