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Found solution here: https://www.gog.com/forum/supreme_commander_series/crashing_after_resolution_change/post2

Just delete config file from "C:\Users\(your username)\AppData\Local\Gas Powered Games" folder
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Whereaminow25: Not sure if this helps, but Since I don't use gog galaxy, I use the offline version, for it to install and play right, I have to unblock the exe, and all parts of the game, right click properties, unblock, apply.
It's not blocked for me to begin with.

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Kernel32.dll: Just delete config file from "C:\Users\(your username)\AppData\Local\Gas Powered Games" folder
%UserProfile%\AppData\Local doesn't have a "Gas Powered Games" folder.
Post edited June 16, 2020 by SKARDAVNELNATE
I have the same problem. The Steam version loads fine but the GoG version won't load.
As already suggested above - remove game folder from ./AppData/... Looks like versions conflict in config file. Steam version is separate version, a bit differ.