Only one GUI toolkit should manage the system menu bar, even though we allow several GUI toolkits to be running simultaneously. Otherwise, bad things may happen (e.g. https://javafx-jira.kenai.com/browse/RT-24453 ).
FX won't use the system menu bar on Mac if the main running toolkit is AWT, and will fall back to using software menus rendered in the window client areas instead.
AWT and Swing's Apple L&F should do the same if they detect that they're embedded in JavaFX.
The corresponding FX bug: https://javafx-jira.kenai.com/browse/RT-37363