Unless it was changed sometime after 1.3, I know what's causing it. The command ordering the drone to dock to the carrier isn't cleared even after it docks. Just look at the docked drones and you'll see they still have the "Dock at..." command running. Manually order them to end that command and they'll come under the M7D's management automatically. Does your method make the Drone have an M (or was it a H?) before their name? Mine doesn't. Drones will still sortie the next time the M7D carries out the "...using drones" command and that's the most important thing.
Still needs to be fixed.