1.) I can not replicate your problem. It may be that I am using a different operating system, or you are using an old version. Can you download the pre-release
  https://github.com/neurolabusc/MRIcroGL/releases/tag/v1.0.20180402
and see if this works fine. The "motor.nii.gz" file should be included with the software. If you have any problems with the pre-release, can you tell me if you are using MacOS, Windows or Linux.

2.) I would always recommend adding the command "reset defaults" as your first. Without this, the appearance may be influenced by whatever you did before the script, and that could lead to inconsistent results. 

The classic script would be:

begin
resetdefaults;
loadimage('mni152_2009bet');
overlayloadsmooth(true);
overlayload('motor');
overlayminmax(1, 2.5, 2.5);
backcolor(255, 255,255);
shadername('overlay_glass');
shaderadjust('edgethresh', 0.6);
shaderadjust('edgeboundmix', 0.72);
end.


or with the new Python scripting included in the pre-release:

import gl
gl.resetdefaults;
gl.loadimage('mni152_2009bet');
gl.overlayloadsmooth(1);
gl.overlayload('motor');
gl.overlayminmax(1, 2.5, 2.5);
gl.backcolor(255, 255,255);
gl.shadername('overlay_glass');
gl.shaderadjust('edgethresh', 0.6);
gl.shaderadjust('edgeboundmix', 0.72);