Hi DinoRS,
Thank you for the post. With regards to the two onboard NIC, have you check with Supermicro for any BIOS upgrade on the board (understand this is a new board already) and updated the driver.
For the standalone X540-T2, have you try using latest driver downloadable at download Network Adapter Driver for Windows Server 2012*
I will check further on the logs.
rgds,
wb