This just started happening after installing Java 1.7u11 and its contained JavaFX 2.2.4, it was OK previously. I have a Group containing a BorderPane with Buttons in an HBox in its bottom component, and a Canvas in a StackPane in its centre component. On the Scene becoming visible, the buttons are visible; however on focus/clicking, they become invisible (all except one) and generally behave incorrectly. Replacing the Canvas with a Rectangle removes the problem. Putting a 3 or more pixel Insets gap between the Canvas and the Buttons removes the problem - this provides clearance around the buttons' focussed border. Adding the BorderPane to the Scene directly instead of via the Group removes the problem. Possibly this relates to Canvas dirty region problems? - e.g.