Tried it with Java8 and Java9. In both is the same bug.
I have tried out the tutorial programs at
http://docs.oracle.com/javafx/2/get_started/jfxpub-get_started.htm
on Linux 64bit.
And that is the result of the popup-window:
http://s16.postimg.org/gt925lvit/Popup_Menu_Bug.png
So the Fancy
So the Fancy Design with CSS with the coded GUI have the popup-bug.
Here the code: http://docs.oracle.com/javafx/2/get_started/LoginCSS.zip
But the same program created with FXML (User Interface Design with FXML)
have not that bug.
Here the code: