If you quit a game while in a boat, the boat will disappear and the player will find themselves in the water when the game is reloaded. I'm pretty sure this is new to 14w07a because I had regularly been using quit/reload as a workaround to the boat desynch problem. I don't believe it's simply the boat despawning between game sessions because an unoccupied boat left in the water will still be there when the game loads. I'm also playing in survival mode, I have not tested this in creative.