I have two installs:
C:\Program Files\Ubisoft\GreyWolves and C:\Program Files\Ubisoft\NYGM
I have two installs of SH3 Commander:
C:\Program Files\SH3 Commander\SH3Cmdr.exe and C:\Program Files\SH3 Commander NYGM\SH3Cmdr.exe
On my desktop I have two SH3 Commander links:
"C:\Program Files\SH3 Commander\SH3Cmdr.exe" /l:"C:\Program Files\Ubisoft\GreyWolves"
and
"C:\Program Files\SH3 Commander NYGM\SH3Cmdr.exe" /l:"C:\Program Files\Ubisoft\NYGM"
So install your SH3 Commander twice into seperate directories. Than rclick on the Desktop Shortcut and change the Target property to add the proper /l:"C:\Program Files\Ubisoft\GreyWolves" flag to it. Do the same for the other copy's desktop shortcut. I usually rename the SH3 Commander shortcuts to "GM" and "NYGM" to tell them apart easily.
The flag is a lower case L not a 1 by the way. /l not /1.
I actually have 8 SH3 icons on my desktop. The SH3 Commander, SH3 itself, SH3Patrol or SH3Gen, shortcut to the install directory, shortcut to the career files directory per install.
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