I had trouble with this at first, too. I higly suspect your using the out of the box version of the mission editor. Patch 1.4b (or the one before?) included a new version of the mission editor that I believe reads the locations.cfg file and shows the actual shape of the ports. Are you using a shortcut for the mission editor? If so, delete it and create a shortcut for the mission editior icon now in you SHIII directory.
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