There is a technical difference between Gigabit cables and 10/100 cables. And the fact that 2 Gigabit adapters don't need a crossover to connect them. So cables are a possibility, the other obvious thing is drivers for the card, but I'm sure that you thought of that. I had to deal with that on Windows a few times and Linux drivers are a nightmare to me.
I don't know what your network card would have to do with watching a Bluray remux on the HTPC, unless the bluray remux is on another computer, but you did not say anything about a network or streaming.
FWIW, I found absolutely no difference on my Gigabit network when I pulled the Gigabit card out of my HTPC and used the onboard 10/100 adapter instead. Either streaming from the internet or from a shared source on my network. My HTPC is older than yours, a pentiumD Compaq with a ATI HD4350 video card.
Has anybody mentioned how dangerous publishing your email address is? Any body that sees it can now legally use it for any reason they want, spamming the world in your name, for instance.