We are close to deploying a fairly major change to the PlayCanvas runtime. It introduces a Layer System which grants you the ability to control the order in which your scenes are rendered.
I recommend that you test your projects against the dev build of the PlayCanvas Engine. See this page for instructions on how to do that:
We have tested this change very thoroughly to ensure backwards compatibility. But if you notice any different behavior when using the dev engine, please follow up on this thread and we will investigate. Otherwise, we should be in a position to deploy this change later this week.