We have been seeing slow performance issues with Microsoft 2003 server and file shares when both are set to gigabit (both the switch and server show 1000 full), but when set slow speed 100 full server performnce is much better.
We had statically set the switch port to 1000 and by default it is set to full duplex. We also statically set the server to 1000 full as well. Things run fine for a while, and something unknown happens and the server response slows down over period of time to the file share resources on the server not accessible.
When you have both set to Gig Full do you see input errors on the switchport ? If so, the server is likely loosing the duplex setting, try looking for a patched driver. Make and model information of the NIC is also helpful.