Well, I haven't heard of this one yet 
Can you make sure your updated and or validate your installs with impulse?
Are you sure your both on the same version? Dip is at 1.011
Unistalling Sins does not delete folders from C:\Users\<username>\AppData\Local\Ironclad Games\Sins of a Solar Empire.
It is possible there is an old mod enabled in the old EnabledMods.txt
The only other thing I can suggest is mods override all other files. Create a folder in the mod directory named GalaxyFix or something then make a GameInfo folder inside that and place a GalaxyScenarioDef.galaxyScenarioDef in the GameInfo folder. Enable the mod on each comp. And you are now a modder to boot.
C:\Users\<username>\AppData\Local\Ironclad Games\Sins of a Solar Empire\Mods-Diplomacy v1.011\GalaxyFix\GameInfo\GalaxyScenarioDef.galaxyScenarioDef
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