When I edit a game's properties using MameUIFX by changing Display>Video Mode>from "Auto" to "OpenGL" and then edit OpenGL>Enable GLSL to checked "on". Then I have to pick a "Main Mame Shader" to apply the glsl shader.
The game starts normally with the bezel and properly centered.
Now to figure out how to apply those changes to all games w/o having to delete all the config files and start over from scratch.