I think I read in this forum somewhere that you had to have the items in your cargo, on your ship, or in the fleet to get credit. Items dropped off at Glory were not counted in your score. Makes sense to a point in that Glory always has three items there anyways...
Now I know why taking stuff back to Glory and dropping it off produces a lower score. The object of the game seems to be to carry as much stuff as possible. You have no base really - Glory is just the starting planet. It is a planet that you must protect and the place where you retire.