Thanks to all for the responses; I am indeed also running win7.
I don't yet know how the work-around will affect things post mission, all the exiting I've done so far has been in mission. I've noticed that when I do load the game (even though it says loaded via SH3 commander) the rank is incorrect in the initial main menu, this corrects after loading a save game. My worry is that, as SH3C thinks SH3 is still running after it's been closed, then the end of the mission won't be correctly recorded in SH3C.
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I use windows10 and I have no problems, have you tried launching SHCmdr with administrator rights?
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I always run both GWX and SH3C in admin.