Sounds odd...
I haven't noticed any drop in frame rate. Trying to think what might even cause that. Are you adjusting the transparency in MoBo, that's about the only thing I can think of that might stress the graphics card.
Have you tried alt-tabbing out of the games a few times and NOT running MoBo just to see if it's an op system setting that could maybe be adjusted?
Personally, I run MoBo side-by-side with SH in windowed mode and I haven't noticed any significant differences in SH frame rate when I return to the game.
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