I haven't seen it happen again. It only happened that one time in that snapshot too. So it must have been intermittent.
I tried it in 15w44b. The server is the same except that Java is not 1.8 Update 65. The client is now Java 1.8 update 65, and OS X 10.10.5.
The boat is no longer sliding in and out of the dirt. It does intersect strangely with the land.
This is an improvement as it no longer goes nearly as far into the land and is not going back and forth. I'll leave it to you to decide if the new screen shot is acceptable.
To take this screen shot, I found a straight section of shore 4 blocks long, and dug the 2-block inlet. So the water there is not source blocks. Then, I placed the boat and moved it out a bit and then back into the inlet and got out.
The boat is stationary, but intersects the shore strangely.
How is this a duplicate? I am not exiting and experiencing the settings not changing.
The settings are changing while I am playing. It is typically, but not always, when I hit Escape and then press "return to game", not exit as in MC-95696. Sometimes it happens while playing without pressing Escape and returning to the game. I just notice the screen getting darker while playing.
I have not noticed any association with switching versions between 16w04a and 1.8. I've never noticed it happen in 1.8. When I press Escape (to pause single player) and then return to game, I am not switching versions. In fact, to switch versions, you have to exit the game, edit the profile and restart. I am not exiting.
Therefore, I disagree that this is a duplicate.