I suspect that this is a CSS bug, but possibly something in layout changed that triggered it. This can be reproduced with a very simple program that has a scene with a fill color other than white, and an HBox as the root node. If you add a Rectangle to the scene, the background remains green as expected. If you add a Button to the HBox (either instead of or in addition to the Rectangle), then the background turns white.

This appears to be a recent regression.