Command discs can contain battery fuel, but there is no way to set their priority. On a multi-staged vessel with several pods, this makes it impossible to control the sequence in which they drain.
Since the game seems to default to draining them from the topmost pod down, it means by the time you separate your final stages they are out of battery charge.
Editing the XML file manually seems to allow the desired control. It should be easy to add the UI for this in the Command Disc's properties, please do so!