Thanks for the suggestion, I will perhaps try this, the complication (as you may know) is that if, on turning the onboard graphics off, the computer does not find the graphics card, the only way I can see to get the onboard graphics back is through a jumper reset (the jumper in case being buried under all the fans) which is awkward, and also resets the hard drives to not ATA (which I had to set them to to be able to get Linux to see the Windows OS) which the causes me to have to reinstall Linux after resetting the hard drives to ATA (not ideal).
I am not sure it is a conflict however, even without the additional (GT610) graphics card installed, I also cannot get output from the CUDA card, which came with the system. It is this that is leading me to believe there is some configuration/setting preventing output to additional PCIe video cards. As you mention it is a bit of an issue, not only will the matrox g200 not support aero, it also doesn't support many other things, such as opengl etc.