Joe nailed it. FSX doesn't save an AICarrier when it saves a flight. The plane, yes, but not the carrier. You have to place the desired carrier after loading the plane with the saved flight.
Actually, best way is to hit Slew as soon as the plane loads. If you use pause, you're likely to get a crash when you unpause. The plane may be slightly above or below where you thought it was, and thus...crash. With slew, you can place the boat you want, then settle the bird down onto the deck, or raise it up above the deck, and then settle it down. Hit Un-Slew and start the boat moving, and away you go.
You will have to be careful of which way the boat points when it loads, though. It may not be pointed where you expect, with the plane in Slew.
Hope this helps...
Pat☺