Some time before an option according to this issue was introduced:
http://javafx-jira.kenai.com/browse/RT-19955 (you can also look at this RT-22093)

So, to hide popup, you need additional click.

MenuButton has a popup, and I have manual tests, where two menuButtons are, and it is needed to check, that if I open popup of one menuButton, and after that try to open popup of the second menu button, first must be hiden, and the second must appear, and only one click is needed.

After that fix, behavior in such case changed. Seems, it needs to be fixed.

Anyway, I need confirmation, that if you will not fix it, it will become a new expected behavior.

Actually, that is a compatibility issue.