I also have this problem. Minecraft 1.9 (on Win10x64.) Final messages: Stopping singleplayer server; Stopping server; Saving players; Saving worlds; Saving chunks .../Overworld; then /Nether; then /The End. No players had left the Overworld.
I also have this problem. Minecraft 1.9 (on Win10x64.) Final messages: Stopping singleplayer server; Stopping server; Saving players; Saving worlds; Saving chunks .../Overworld; then /Nether; then /The End. No players had left the Overworld.