You're spot on, exactly >because< it always respawned at the same time it now will not - because the game did not SAVE the location, it simply always spawned them in on its own - on the new version, it tries to load the last known position, but it has not been saved in 0.0.81 sooo it does not work :O
So when you start a game, the new default game will ONCE spawn them in and THEN SAVE them, so they will not disappear again --
However I had it happen to me that the dark crystal was pushed in a wall by me and then it was gone :P