If you be better if you mentioned your exact hardware, the nics, and the switch?
If a Physical Adapter can't be easily detected as 1000 by default-auto, then something is usually causing it to stay down at 100.
In order of most likely cause to least likely:
-Have yet to do a cold reboot of all hardware
-not up-to-date drivers
-Desktop grade physical adapters
-Home-grade ethernet hubs
-old patch cables and/or old ports in the walls.
For example, I've always used Hp ProLiant servers on Hp ProCurve switches, and I never had to do anything to get them at 1000, they simply are by default.