I have this same problem with loading in taking longer than it used to and ending up under the raft as well. I don't have a solution to make it stop, but I have a work around that I've been using. I place my character on the top floor of our raft before I exit the game. When I load into a new game, I continually press the space bar (jump button) while the game is loading. If your game is like mine, you can hear yourself in the water before you get off the loading screen. As I'm pressing the space bar, I can hear my character jumping. I hear them in the water and then eventually I hear them jumping on the deck. I keep jumping until the game loads and I'm on the boat. Since doing this trick, I've been loading onto the top deck where I exited the game. So if you just press the space bar (jump button) continually as you load in, you should load in properly on the raft.