OK, Flag4, try this:
Under the Auto Start tab, make sure SH3Cmdr.exe is set to "Monitored". If it isnt, double click the line and a dialogue box will open up where you can set it.
Then, on the "Optimisation" tab, under "Msc options", where it says "After monitored programs have been closed" select "Pause processing" in the drop down menu.
Now when you close SH3 and Sh3 Commander, you will be left with the Alacrity PC box. Just type "X" and it will restart everything. (Note: your wallpaper might restart before it pauses, but other than that it should work fine).
Let us know if this sorts it out.
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