It appears there were two separate issues, the Pro/1000 GT was faulty (MAC was FFFFFFFF) and kept insisting on installing as 1000 MT, and the 14.5 diagnostics SOMETIMES said a pair was missing for high speed operation on the other NICS, however despite the problem only appearing with these NICS in this Switch and not other NICS in the same Switch SD2008 Linksys, switching to another similar SD2008 switch - the problem went away.
The faulty NIC could not be configured under Hyper V as a virtual LAN - which is how I found it was faulty.
No Lightning here for some time...
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Some people ran into a similar issue recently with one of the desktop boards.
They installed the version 14.6 software to fix it. Might be worth a try. Even though the software is listed for desktop boards, it should still work since the Ethernet Controllers use the same driver packages.
Not sure if you are running Server 2008 or Server 2008 R2, but here are the packages that will work.
LAN: Intel® PRO Network Connections Driver for Intel® Desktop Boards for Windows 7* (The x64 package works on Windows Server 2008 R2.)
LAN: Intel® PRO Network Connections Driver for Intel® Desktop Boards for Windows Vista* (The x64 package will work for the x64 version of Windows Server 2008.)