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Gentoo + gigabit ethernet?

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Gentoo + gigabit ethernet?

Using a gentoo LiveCD I managed to obtain 20+mb/s off one of my servers, however, if I boot it into gentoo (off a disk) using my kernel, I can only manage to get 100mbit speeds (it maxes at 12mb/s) even though the card is gigE (and can give 20+mb/s). What kind of things should I look for in the kernel to see why it will not give GigE speeds? (ethtool shows it as 1000FD so its not that its not seeing the card as gigE)

The card is an intelpro PCI gigabit card.

Cables and swtich are the same for both tests, so its not the hardware, it must be the software.

running kernel 2.6.13.3.

Any help will be greatly appreciated.