Oh, about mods... FL seems to want to restart the whole singleplayer experience every time a (slightly) different combination of mods is used. Wazzup widdat?
Go into your My Documents\My Games\Freelancer\etc. until you get to a folder that says "OriginalSavedGames". Copy all the files and drag them to the folder above.
Roger that. *Shakes a stick at the silliest directory ever*
... Um... I... have a whole bunch of folders... somewhere around there... I feel crazy.
H-hey, no OriginalSaveGames! Only separate mod-save-directories... Well, I see which files are savegames, no worries.