I noticed that when you switch scene (HXP.scene = new YourScene()) There is a "flash" where you see just the background colour for one frame. And then the scene renders. If you add this trace:
To Scene.hx render() function line 160, then when you change scene you can see that there are 0 layers for the first frame.
This flashing gets annoying when your game has multiple little levels.
Not quite sure what the best fix for this will be... Trying not to render a frame if the layers are 0.