Yeah sorry about that. I probably should have been more descriptive. Obviously, the models for the 2 front seats in the upper deck and all 3 seats in the lower deck were missing (even though the crew slots for them were still there). Jeb's model is still there but Bill's is absent for some reason. I unbuckled Jeb, and floated throughout the cockpit (I had the zero-g cheat on at the time) and he was able to sort-of no-clip back in. I maneuvered Jeb back to his "seat", and he returned to the same weird horizontal no-clip position.
Also, I do have habtech props.
Log: https://www.dropbox.com/s/8r885s466tj3s6o/KSP.log?dl=0
