Dealing with this exact problem, Dell Poweredge T610 network card (bnx2 driver) kept negotiating down to 100 Mbps. If I forced it with ethtool it would work fine for some "period" of time at gigabit speeds, but then suddenly renegotiate downward. Turns out I had tuned installed and set to powersave mode. I installed tuned so long ago I had forgot about it, and your little mention of it made my brain hamster wheels spin. So far so good, I was ready to cry and get the motherboard replaced .
Thanks alitvak69