I had a similar problem with my 82579V Gigabit NIC refusing to negotiate above 100Mb/s.
This was in a computer-to-computer LAN, direct connection with single cable, no router.
After trying various cables, I've come to the conclusion (completely empirically) :
. it is not related to cable quality (Cat5e and Cat6 work equally well)
. it is related to cable core connections - straight-through or crossover.
if straight-through, it connects but not above 100Mb/s.
if crossover, it connects at 1Gb/s
I guess the MDIX logic for doing the crossover itself (for the straightthrough cable)
conflicts with the higher speed.
So - check your cable core connections are correct for the NIC on the other end.