Yeah, that's because the issue you're describing occurs when a folder or the .bat is placed in the wrong location, so it wouldn't be an issue with the game itself or the files, just where they are. The .bat has to be in the same folder as swfoc.exe, the Mods folder has to be in that folder as well. Then the Imperial_Civil_War folder has to be in there, then it should run with the bat. Common errors include people having an Imperial_Civil_War folder inside the first Imperial_Civil_War folder, so it ends up as: \Imperial_Civil_War\Imperial_Civil_War\Data, which is incorrect, or leaving the .bat in the Mods folder.
If that's not working, you can potentially try changing the contents of the bat to:
swfoc LANGUAGE=ENGLISH MODPATH=Mods\Imperial_Civil_War
But I don't think that's necessary. I don't own the GoG version, so I don't know. All I know is that the mod works on it, and that the process should be the exact same as the retail disk version.
The ICW.bat is in the same directory as swfoc.exe, i have tried putting the .bat in the other files with the mod, im still unsure of what you want me to do.
I just tried changing the contents of the .bat to what you said to no avail.
Heres a picture of the directory and inside the mod directory.
http://imgur.com/a/2yN3H