They all have different structures, because the load different. My problem was because I was trying to make a mod that loads in the mods menu, I had to create a folder of the same name of the pk3 in the Gamedata folder.
My map pk3 is "r5" so
This extra folder and placing it in Gamedata is vital. Not one tutorial that I read mentions this.
So when you zip your map for distribution. (if your doing it this way loading in mod folder) Have this "extra" folder in your zip file so it opens on their computer just like yours in the GAMEDATA folder not BASE.
Base can cause problems with other mods.
Could have saved me 12 hours if I knew this "rare fact" sigh.
Oh well I hope this helps someone else....