This MUST be done to be able to create and play skirmishes that use more than one region!  
Open your config.cfg file in your X-Wing Alliance folder.  Change the following:

each_team_own_region 0

to

each_team_own_region 1

This seems to do two things.  First and foremost the player always starts in its teams' region.  The second thing it seems to do is make sure computer opponents follow you to the correct region when you are fleeing or are ignoring them.  Not enabling this seems to make the computer opponents search the regions in a set order until they find you.