I'm not sure what you're problem is about mod manager and it seems strange but anyway. I hope this will help. Below are how to fix some of the problems with mod manager. See if you have had anything like it describes.....

If you ever got a message saying that this mod could not deactivate properly then go to tools and restore backups. This will make everything OK again.

Make sure you have deleted ALL saved files with that mod on. This INCLUDES autosaves. An easy way to delete the autosave is to go to the 'tools' tab in the freelancer mod manager and click 'delete autosaves.'

If you have tried to go online with a mod on then it can sometimes do this. Mods sometimes do not agree with the server or need the server to have the same mod. This can sometimes cause freelancer to exit.

Hopefully this will help you. If you have further questions then E-mail me. Good luck!

Look out for SE6, SE9 or SE10 online.