Hi!
I a have Intel s2600wt motherboard this two X540-AT2 ehernet adapters. Link speed in auto negatiation is only 100mbps, then i set 1000mbps on switch or in ethernet adapter properties - link lost. My os is Windows Server 2012 R2 and my switch is Cisco 6509 running on ios version 15.1(2)SY9. Also i tried Cisco 2960G with ios Version 15.0(2)SE8 this same result.