This is called color flashing, and it is sometimes unavoidable. You apparently have an 8-bit display on your workstation. This means the hardware supports 256 simultaneous colors out of a possible 16 million.
As an example, what happens if MAE is using 256 colors and your other X applications are using some combination of 256 different colors? The X server notices which window has the colormap focus and loads the hardware colormap with the corresponding set of colors. Change the focus to a different window, and the server loads that window's set of colors.
To avoid this, use fewer colors or get a 24-bit framebuffer. Note also that the MAE General control panel has an option to help reduce flashing, but it has limitations.