I think that you are hit by http://javafx-jira.kenai.com/browse/RT-19435
There is 2 possible workaround there.
1) Don't add the CSS file to the stylesheets property of the container. Instead you need to add it to the Scene.stylesheets property.
You will need to do that in JavaFX code in your application. In order to visualise the styling in the SceneBuilder, you will need to set your CSS file thanks to : Preview/Preview a Stylesheet... When added for Previewing, the CSS file is not added to the running application That is why you need to do it by code.
2) You could add the declarations to the style property of the menuItem. In your case (there is some pseudo states) you will not bet able to set all your declarations.