Well, after much diagnosis. I figured it out. It was the Video cable.
Well I am getting screen flicker on my Sharp 8.4 inch VGA display. I have the display hooked up to a power support connected on my DC-DC PSU. Could it be that it needs ground instead of -12 that it is getting?
I thought that it was heat and drilled holes in the top of the case and it is still doing it.