Just to add to this - I posted a similar thread (not having seen this one) and someone pointed me here.
We are also running vSphere 6 with Windows Server 2012 R2. We spent several days looking for answers, and simply disabling LRO on the NIC in the OS fixed our problem.
Thank you all very much for your input - it's been of great help. I'm a little disappointed that VMware haven't put this in a KB article - they are normally very good at this.
Does anyone have any idea of fix dates? I guess the fix will be in the form of an ESX patch, at which point we will want to re-enable LRO on the NIC.
Thanks
Ian