We would like to inform you that server 2008 R2 standard is not a supported Operating System for this platform so the troubleshooting we offered is limited:
Our best recommendation to narrow the issue is testing with a fully compatible Operating System.
I've also had issues with the NIC on this motherboard however I was running UEFI. I had to try and get Secure Boot to reload all keys before the machine would boot with an active NIC.
For a short time, if I cold booted, the NIC would not be present. I had to warm-boot and on the 2nd boot, the NIC would appear and be available. It was a pain to have to do this workaround until I found out about Secure boot.
Problem I have to day is that I configured Hyper-V on Win8.1 Update and now I have the same issue again with have to boot twice. I have the latest NIC drivers and BIOS update so I don't think this is the issue.
This motherboard is temperamental!