2Korn,
Did you delete the saved MP games? (that's what usually crashes mine after mod testing and switching back/forth). You can just delete them from the mydocs\mygames\freelancer\accnts\multiplayer\ folder. Inside that folder is a numbered folder for each account that played on your server. Inside that folder is a numbered file for each character created (they are date-stamped by save). Just delete the ones you created while using mods. Same goes for SP saves if those were the ones you used to toy with mods.
Remember, game saves made with certain mods will often crash FL when the mod is overwritten or changed. To be safe, I always start a new toon for testing and delete him at the character screen before I exit the server (if you know you're changing mods).
Hope that helps.