Thanks for all the answers guys

Anyway, for any others interested in this, I have finally found the answer. It seems that either most do not have this problem or are highly skilled at these things. The problem is where the map defaults to save - at least for some people.
The defaulted spot C:\Program Files\Stardock\TotalGaming\GalCiv\Mods\Default
is incorrect and should be through
Twilight\Data\CustomMaps\
YourmaphereSo, act23456, load your map on the editor and resave it through this file and you should be good to go