I'm hitting the same bug, except I also lose my staging stack and the burn meter to the right of the navball. My ship has no nuclear engines, however. I've got KAS, KIS and MechJeb2 installed. My ship has a Hitchhiker Can, a basic Command Module and a Probodobodyne HECS. I leave the ground with four tourists and an empty command module. The issue occurs when I rescue a Kerbal from orbit. As soon as you press "B" to board the Kerbal into the empty command module, the staging stack disappears along with the burn meter and the crew roster. The Kerbal gets cloned and is still hanging onto the command capsule, but he's actually inside. You can complete the mission without the staging stack, and the rescued Kerbal is actually inside the command module.
