Why is it that the Planet Express Ship is on personified in the episode "love and rocket" but never in any other episodes?
In that episode it suited the plot to have the ship possess an AI and a mind of its own. In all other episodes it would either get in the way or be more time and effort to make logical than it is worth.
So it's introduced as an upgrade to the ship's software, and removed later because it has minor homicidal tendancies and employees get antsy about co-workers that they do their jobs inside of trying to kill them.