The same here for me and i have a pretty decent gig. First the Cyclop never load when resuming a saved game, now this... And since the loading cyclop bug is pretty old and even made through the stable branch (seriously, who update a "stable" branch …
Just for information, i tried an new savegame since then and the problem is the same wiith the Cyclops. If the seamoth is inside, it disapear too (and i was on board the cyclops).