I've got a Gigabyte GA-X79-UD5,
It has the EXACT same problem described here.
Situation :
120mbit/s ISP
D-link dir655 router
Cat6 wiring in house
Old computer (Intel X38 mobo)
New computer (Intel X79 mobo, Gigabyte GA-X79-UD5)
Both computers configured as "Auto-negotiate".
Both computers run W7 x64 SP1
Problem :
Old computer gives a max. speed of 119mbit/s during download.
New computer gives a max. speed of 50-60mbit/s during download.
Tried :
Different drivers (16.5,16.7,16.8 )
Different OS (Ubuntu 11.10)
Configured link speed for 100mbit/s full duplex, which as pointed out here works perfectly (100mbit/s during download).
State of mind :
Not amused
If anyone can tell me more about this issue and whether or not this can and will be fixed with a bios update, that would be great.
I'll wait about 1-2 weeks on this and then I'll RMA the board if no solution is given.
Already contacted Gigabyte support directly as well.
Hope the best for all of us

Crossed my fingers hoping that this will be fixable with a bios update and not a new motherboard revision.
Else all that remains is an RMA.
Also here are some links to what appears to be the same problem with the GA-X79-UD3 ! :
http://forums.whirlpool.net.au/archive/1834185 (tried 100mbit/s which "fixed" the issue like us)
http://forums.guru3d.com/showthread.php?t=355177 (this guy didn't try 100mbit/s)