Pressing 'Play' triggers full recompile and breaks game

I've just upgraded to 5.6.1, and now ever time I press 'Play' it enters play mode, but then immediately decides to recompile all the scripts and reload them, which of course means that I get a billion NullRefExceptions as all my script properties have been dropped.

Nothing is changing on disk (as far as I know), and there doesn't seem to be any editor tools active at the time. This happens on an empty scene. What can be causing this recompile and how can I track it down or stop it?

Thanks