I've just started a new game on 0.99j7 and came across this odd event.
When I went to a Church mission - Temple of Sirius - the one where you start without your ship, I was supprised to start with my ship, even though the breafing says you always start on foot.
I made a save of this, and then reloaded - same result. I then tried several more times, aproximitly half started with the ship and half on foot.
included the mission save and a geoscape from just before the mission.
Any idea what's up?