[Edi]

The onbly things you can do in the map editor are assigning terrain types and neighbors and setting province names. Nothing else.

You need to edit the tga in an image processing program so that there are those (255, 255, 255) pixels where you want the province flags. And like Gandalf said, make sure there is only one, otherwise there will be two different provinces in the same location, as I learned the hard way when I had done all the terrain modification on the Faerun map and started on the neighbors assignment. Almost threw my monitor out the window at that point...

Using the map editor every once in a while when you are editing the tga is also a good way of checking if you've still got stray white pixels anywhere. The Faerun map would again have been impossible without it.

One more note: When you've got the image file ready and assigned province names, terrain and neighbors in the map editor and start on the manual map file editing, do not ever use the map editor to modify the file again. If you do, it will cheerfully obliterate everything you added manually, such as special provinces where you assigned commanders, garrisons and other stuff. I learned this the hard way, hopefully you won't have to.

Edi