https://jira.secondlife.com/browse/BUG-4242
That was my ticket on jira.
Now I've had a bit more time to work on this issue, I have found that during my testing the aircraft I made goes spazzy during a sim crossing is still showing it's physics as "ON" according to a monitoring script.
If I "stop" and "Start" the main engine script whilst still seated on the aircraft, it proceeds to continue spazzing out. If I unsit and then sit on the vehicle again, it works normally until the next sim crossing that spazzes it.