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I too am having the same issue. I have a Gigabyte X79-UD7. I believed I had the issue resolved from BIOS revision F6 onward. I have since upgraded to a 50Mbps broadband package with my ISP and the issue returned. Erratic WAN throughput unless manually set to 100MBps Full Duplex. In auto negotiate or manually 1000Mbps I receive roughly 25-35Mbps. When manually switched to 100Mbps Full Duplex I receive my rated 50Mbps.
It was suggested that I try the newest Intel drivers located here. Unfortunately in my case it did not resolve the issue. I am currently working with Gigabyte Support but so far it hasn't paid off. Unfortunately in my case all of my PCI-E slots are used by my graphics cards so I am unable to get a secondary adapter to bypass the onboard.
I know this isn't much help but you are not alone in having this issue.
I'm kinda glad that someone else found this problem. I tried the 17.0 drivers and they do actually help with the problem. You have to set the number of Queues to "1" instead of the default "2" in the card's properties, in the device manager. I am getting about 45 mbits now yet not as stable as the PRO/1000 PT card. And I suspect there is more involved than just the queues, but I did not have time just yet to set up a totally fresh copy of Windows 7.
So far that trick works in Windows 7 and XP. It MAY require setting defaultsendwindow and/or defaultreceivewindow in the AFD service to something about 500,000 to accomodate the bandwidth. As soon as some certain defaults are involved the onboard chip seems to get out of it's comfort zone, so to speak. I wish I could say more about specific parameters...
I did a lot to get Gigabyte to do something, even went to the exhibitor restricted area of the CeBit IT fair and talked to some Michael Linden about it. He told me too that the bug has been resolved in an earlier BIOS but asked me to email him the details. No reply. My attempt at approaching the regular support in hamburg, Germany, was a little more successful but by now they apparently have shrugged it off as oddball phenomenon I suspect. I will make sure tho to forward the URL to this thread to them. The wrote me last that their center in Taiwan tried to reproduce the problem on some 50 mbits line but they couldn't.
Mr. Linden also told me that this has already been fixed, but I just know it wasn't for me. He also mentioned that this was happening when the PCI express bus was getting under high load, for example graphics, which would somehow bottleneck the bandwidth to the onboard NIC.
BTW, I have never used anything older than BIOS F7 due to the potential failure of the CPU power MOSFETs. So far I tested F7-F10 and F10c.
Maybe we can figure something out by the type of internet connection we have. Can you post specs of your line? Cable? DSL? Provider?...Like for example is triple play (Internet/phone/IPTV) involved? That could mean they are using multicast like the German Telekom. How about VLAN tagging? Anything that our lines could have in common...
Thanks for replying!