Your machine sounds very customized. I would recommend trying a different flavor of linux - probably a linux that is optimized for your 64bit processor. Knoppix is a great distro, but I have found that it works best on machines that have relatively simple, standard hardware. Since your machine is using so many high-end parts, a CD-based distro is not very likely to include the software necessary to power all of it. Try something more robust like Fedora Core 3 or Suse.