Actually, no. I checked all 3 of those boxes, and all those options have worked for many months of all my Alts. Except this character. And the test that I did to see if I was seeing something funny was to ride back and forth TWICE BOTH WAYS between Limsa and Vesper Bay and note that I saw cut scenes on all trips. And this was not the first set of trips between those points using the ship. So there's that.

So I gather from your replies that you are not seeing this anomaly. Good to know.