If you mean your custom maps, you'll need to fix them to be compatible with Entrenchment. To do this, do the following steps:
1> Go to the Galaxy folder. In XP, this is usually C:\Documents and Settings\(you)\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Galaxy\
2> Open each .galaxy file in Notepad
3> The second line of each file will say "VersionNumber 2". Change the 2 to a 3.
4> Save it.
5> ???
6> Profit!
Okay, ignore the last two steps. That's it, nothing else seemed to have changed between the two map file versions, at least on the test case I made.
If you're talking about the pre-made maps, then no idea, try reinstalling.