This might not help with exactly the setup you have but might at least forestall worries about the wrong issues.
I installed Red Hat 7.3 on an AT7 Max with no problems. Well, I chose a bad video setting at the end, and the install froze, leaving me to muck around figuring out video card/monitor settings and finishing that bit manually before I could run X, but that's it - no motherboard issues. All new computer components, incl. USB keyboard and mouse - just plugged them in and started up.
So that's a different distribution (though I have the same processor, incidentally, and it's running in spec; same cooling, too), but it indicates that there's not, in general, a problem with this non-legacy motherboard and Linux. Oh, also, I have not disabled USB 2.0 or anything else - motherboard running defaults out of the box, IIRC.
Do you know that the rest of your system works otherwise? Can you try installing your distribution on a different system? It would help to isolate the problem if you know that the hardware is fine with a different OS or vice versa.