Well, this usually happens when you use a map placed in the galaxy folder under either:
C:\Users\username\AppData\Local\Ironclad Games\Sins of a Solar Empire\
C:\Documents and Settings\username\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\
and not in the galaxy folder in the place where the game got installed.
If this is not the case, it's probably because you've either tweaked the GalaxyScenarioDef.galaxyScenarioDef file too much or the planet files itself.
Try creating a custom map with either the ingame editor or the GalaxyForge while using your own changed GalaxyScenarioDef file.
At least, that's what I imagine that could help.