I did have the same thing happen to me and it's cause was an OLD mapdesigner map, which I deleted then even map designer worked. to find and remove maps that can offend please follow these instructions
you have to remove ALL galaxy files older than 20 feb 2009 in
(C:\Program Files\Stardock Games\Sins of a Solar Empire\Galaxy(32 bit) or
C:\Program Files (x86)\Stardock Games\Sins of a Solar Empire\Galaxy(64 bit)) AND
C:\Documents and Settings\"user name"\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Galaxy (xp) or
C:\users\"user name"\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Galaxy).
an alternative is to do a windows search of the hard drives for all galaxy files (ie *.galaxy) then click on more advanced options and put a tick in search hidden files & folders BEFORE clicking on search
hope this helps
harpo