I've noticed that a lot of maps that come with the game don't show up until you re-save them. Typically by then I've done a little editing to the environment and replaced all the starting locations with new ones. I'm not entirely sure why they don't show up to begin with. If you start with a blank map, build it, and it still isn't showing up, then I'm not sure what to tell you. You're placing starting locations, right?
Starting Point 1 (red) will be for you, 2-8 (green, black, blue, etc) or however many will be AI, I think in the order they appear in on the selection screen. Which means if Altar is in they'll be Starting Point 2 (I think, don't quote me).
The map creator is buggy as hell. It got a little better in 1.19d (I can go from the editor to a new game, but the editor will crash if I go back in before restarting, before I could never go from editor to game, always had to restart), but I have faith SD will eventually sort it out.