Thanks for the report.
Where are you running Wireshark? Are you watching from a mirrored port on the switch or is it running on the server? You might not see the 802.1q tagging if you are running on the server because of VLAN tagging offload. See http://www.intel.com/support/network/sb/cs-005897.htm.
We will also test the taggine here at Intel. I will let you know what we find.
Thanks for the link, but as it turns out this is what has been causing my issues! Or at least a combination of the that and a layer 8 issue. I have found the NICs work as expected with the VLAN ID tagged in the 802.1Q header, but only when the 'monitorMode' is DISABLED on the sending NIC. If you enable the monitor mode on the sending NIC then they seem to get tagged under the ISL header rather than the 802.1Q header. This can easily be observed by connecting the two ports on the server via a crossover cable and sending out a packet through a VM in hyper-v. I'm not sure if this is intended, but it got me confused for a few days.
I know what people are thinking, why the hell would anyone enable the monitor mode on the sending NIC? Answer, I had been doing some monitoring previously on that port and that setting was still enabled. So the moral of the story is make sure everything is set to default, including settings in the registry, before creating a report.