Roland,
There is very good chance that this is simply an issue with the board design. On early PCB revisions (C and earlier), there was a known problem where the National PHYs would only negotiate up to 100Mbps, even when configured properly for supporting 1000Mbps. Revision D and later were supposed to have made adjustments to improve the PHYs ability to properly support 1000Mbps.
You can try the other port on the board and see if you get better behavior, or I would recommend working with your local FAE to see how you can get a replacement EVM.
Regards, Daniel