One thing to double check.. is the CABLES as well.
Even if you have a gigabit device on the end.... if you are running a cat5 only cable.. it will not support the full speeds, and likely force it to linking at the lower speeds.
On another forum, a user recently had 3 cables. Cat5 gave the slower speeds as expected... they had one that WAS labeled at 5e... but did not link properly either. They got a cat6, and it worked fine.