Yes that did it!! Thank you very much for the tip firath.
Everyone, all your problems are probably the same problem.
Delete your custom maps from the Sins\Galaxy folder and from either:
C:\Documents and Settings\username\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Galaxy
or
C:\Users\username\AppData\Local\Ironclad Games\Sins of a Solar Empire\Galaxy