That surprises me; I thought you could disable onboard graphics completely and just tell it to "look" at the PCIe slot or whatever and that was that. Are you sure it was properly disabled?
Sorry, you said you had an issue building your MythTV, but then you said it worked fine with Myth and caused problems with LMCE - could you clarify please?
Sorry about the confusion. I had memory problems with setting up my MythTV. It was a Hauppauge issue when you installed the latest nVidia drivers and also tried to get component out. I had to edit the grub to reaollocate memory on boot up so the the nVidia drivers had room to load. Once I fixed that in Myth, it was fine. That was the only real issue but it was well documented.
The LMCE issue was because the onboard Intel GPU wasn't cutting it, when I looked in the BIOS to try to bypass it, it only allowed me to put the onboard as a secondary priority and not disable it completely. This particular problem didn't seem to cause an issue with MythTV but LMCE didn't like it. I even connected a monitor to both outputs just to see what it was doing. If the onboard GPU was set to the primary, it would install and load just fine. I just had perfomance issues with HD and the nVidia card had no output at all. If I set the nVidia card as the primary, then I would get to the video wizard and and it would just hang. I couldn't seem to get it to show on the screen. I know that there are instructions for hitting the right keys in the right order to get a screen to show up but they didn't seem to work. I could dig through my docs and find the MB model and also tell you what it says about the video options for the BIOS.