I spent time last night and this morning trouble shooting this issue. I tried resetting the BIOS to defaults (my system is overclocked), but this did not correct the issue with one adapater no longer working in Windows.
I downloaded Intel's DOS utilities from here: http://downloadcenter.intel.com/Detail_Desc.aspx?agr=Y&DwnldID=4237&ProdId=992&lang=eng. Now this will not run under 64-bit Windows at all. I am not sure about 32-bit Windows, since it is a DOS app. Luckily, I have all equipment needed for thorough diagnostics (a USB bootable powered drive containing MS-DOS 6.22 and an ethernet crossover cable).
I copied the files to my bootable USB drive then rebooted my computer with it attached. I ran the diagnostics utility, identified both adapters on the motherboard via the blinking LED test, then tested both of them. Both ethernet adapters passed all test except for the two network tests when connected to my FIOS router. This tells me that the adapters function correctly, but there's something else causing the issue.
After reading the information presented on screen from the DOS utility, I connected my ethernet crossover cable to both adapter one and adapter two. I then ran all test including the two network tests for the adapter that was not working in Windows 7. It still failed both network tests. I figured the motherboard needed to be replaced again. I powered off the desktop.
Out of curiosity, I connected my FIOS router back to the adapter that was not working in Windows then powered the computer back on. Guess what? The adapter is now working again in Windows. I can only guess there was an issue programmed into the adapter that the DOS utility managed to correct some how.
I have no other clues as to what went wrong here.
This same ethernet port is now not working again.
I powered on my desktop this morning to find it showing a message in regards to it failing POST, I did not re-enter the BIOS setup at this screen and instead powered the maching off. I waited for a bit then powered it back on. I received the same POST failure. This time I re-entered the BIOS setup without changing any of my options. I saved what is currently set then exited the BIOS setup. My desktop then booted into Windows.
After all of this happened, ethernet port 1 is now not working again. I am connected via a wireless connection (I was wondering why this motherboard needed a wireless connection; now I know). The ethernet port is currently hosed. I tried using the BIOS defaults before, and this did not help.
I initiated an online chat with Intel support. The motherboard is defective, and they wanted to start an RMA for it. This is RMA #2 for the same motherboard model. I'm not going to RMA this board again and have a third one sent to fail again at some point in the future.
For now, I will live with this failure. I will look to replace this motherboard with a more stable and higher quality motherboard as more issues start in the future.