I am not sure wether it is just Vista or all OS's, but if the loading of your map files fail you have to empty or rename your cache folder each time you want to load a new/changed map, so extending or replacing of the map folder doesn't work. When it comes to the colormap-files I can't help you, but hoppefully someone who can will stop by. All I know is that they have caused quite some grief in the past.
I am not entirely sure I understand you questions but have a look at this thread as we cover most of the map related subjects in there.
I was just about to post about the same thing, after I had checked if it was you on the original thread.
It works on vista 64. Its a lot easier to just overwrite the whole map directory rather than running half of it from the mod directory.
EDIT: Have you learned anything new from editing VII and HOI3?