Do you have the speed set to auto-negotiate in the NIC properties page? I'd set it to manual, 100MB (1000MB if you have a cat5e cable), full duplex. The other thing to look at is if your server NIC has QOS enabled.
Both are set to auto negotiate. On the Windows Vista computer, I'm able to change to 1000 Mbps Full duplex but not the Windows 2003 computer, in the manual it says "Per the IEEE specification, gigabit speed cannot be forced. It can only be auto-negotiated." I also set QOS enabled on both NIC. The transfer speed 2003 --> Vista remain at 8 MB/s and Vista --> 2003 remain at 40 MB/s.
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