I've been talking with some of my engineering and development folks. We are unaware of an incompatibility between W2K12 R2, X540, FCoE, and the N5K. However, my team flagged "the latest upgrades". When FCoE is is installed, the the MS updates aren't recommended...especially for adapter. If there's a need to update any Intel component in the stack including the NIC or FCoE, the user should only use the Intel installed software or the results may be unpredictable.
Can you provide a memory dump file? I can probably get one of the developers to take a look.
Also, can you tell me if you picked the network driver from the ms updates? If you did, can you re-install the latest driver pack again now that your MS updates have completed. The MS network driver may be older then the one you loaded from driver pack 19.1.