I have no idea whats going on with your system, I was having similar problems during one of my installations. I must have done a dozen format-&-installs over the last 2 weeks and sometimes the onboard NIC worked, sometimes it didn't, and sometimes I would have to swap the cables over every time I rebooted.
Anyway I just wanted to thank you for the link you posted earlier. By trying the steps listed there I managed to get both my NICs working at the same time.
Oh, just thought, I'm sure you've already tried it but I did have some success at one point by swapping the interfaces over in the webadmin, and then swapping them back again. Worth a shot??