https://drive.google.com/open?id=0B0...nd6Z1R3VFZkY1k
This is a link to a save game where I am in the Heavy Transport in Achilles system just prior to taking over the Pirate transport from the wild dogs. When you load it, continue flying to the waypoint and wait through the scripted event. When your option pops up, decline the switch to the new mothership and after the cut scene you should see what I am experiencing.