Can you post a few of your PNG files so I can see what sort of coding is in it?
Also you can put "-basicgui" in the shortcut to MDX to make it run in GDI+ mode, which is how the Configurator displays it.
Default is using DirectX, and it requires your hardware to support transparent layers and such. A 10 year old video card wont render correctly so forcing it to use "-basicgui", everything will be rendered on the CPU not the GPU. What sort of hardware is it on?