Try updating.

Check out the latest beta's of the Freelancer S.D.K. 1.5 and Freelancer Explorer v2.x

Ok you need to make a Dll File, it makes it by it's self and asks you what you wan to name it. It should be right next to the Data file. You only need to make one of the Dll and you use the same one. Becasue..The Dll file can hold as many names, So all you need to do is apply changes every so often and there ya go it should work fine.

I messed up before and if you gotten very far into your mod then it might be messed up.
I had to start all over to fix this problem and good thing I wasn't too far into the mod.
You might see like the names are mixed up and you go back to rename them and make a new Dll. Well that's what I did and it messed up all the names becaused I didn't know the Dll can hold as many names as it could, So I kept making new Dll files and it wouldn't should the names or they would be mixed up.
So the best thinhg I know to fix this is to start over on your new maps / bases/ mod.
If anyone knows how to fix this another way, come and help.