Have you installed SH3 and/or SH3Cmdr to your "Program Files" folder? If so, that will be why you are having problems. Ensure that you install SH3 and SH3Cmdr *outside* of "\Program Files" if you are running Vista/7.
If you have installed both outside of "\Program Files", then I don't know what could be causing your problem - SH3Cmdr R3.2 is certainly compatible with stock SH3.
Let's eliminate the likely possibility first though...
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