Hmm... don't know if it makes any difference but Commander shouldn't be pointing to a shortcut, it should be pointing to the game directory - the folder where the Sh3.exe file is located.
I have three different installations of the game and IIRC I was using Display Changer with all of them, they each had their own dedicated installation of Commander and it always worked fine.
OTOH I had to do a LOT of tinkering to get the game to run the way I wanted, at the desired resolution in fullscreen without being rescaled to a WS aspect ratio. Maybe there was something else I did that helped.
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