Using LSTools to edit characters does not work 100% properly. I have a char that has the talents "Pack Mule", "Opportunist" and "What a Rush". When I load the saves globals.lsb of a save with this char and go to the character editor and just press save changes and afterwards save the global.lsb the talent "Pack Mule" is removed!
Works fine for me. What version are you using? Can you attach a savegame that breaks when saving?