13w39b World Not Saving

The world is not being saved when I click "Save and Quit to Title"
Seems to only happen on a flat world I made, also does not happen 100% of the time.
Progress of buildings and commands entered into command blocks do not get saved, and/or are reset to how the world was the last time it was saved.
On the world I use, I go from survival to creative, and adventure mode.