I tried installing Cybergraphx v3 and I get the same thing. I can go into Screenmode and pick the CGX modes and it switches to them. But on a reboot or cold boot it doesn't 'keep'.
Have you tried force deleting the screenmode.prefs file, then saving the screenmode? How about SnoopDOS? Sounds like a software problem to me (2 motherboards, 4 accelerators, 8 gfx cards, etc..)