This is where it gets confusing you have 2 galactic civilizations folders one is in the program files x86 the other is under libraries\documents\my games i'm pretty sure it wants the second place since it says my games. In case I was to confusing I will repeat myself This pc\ documents\ my games is the right folder.
Actually the star trek mod makes changes to both folders.
the [for your games directory] modifies the original folders (mostly just add designs and changes color schemes)
the [for your my games directory] is for the documents folder.
Still have the original files I downloaded