I use the NetBeans 8 wizard to create an FXML file as documented in the Getting Started
- New > File
- select JavaFX - Empty FXML
- select issuetrackinglite package
- select IssueTrackingLiteController
- select IssueTrackingLite.css

You get an FXML file with an AnchorPane as root element (attached Emorej-initial.fxml).: open it with SceneBuilder.
Now:
- select the AnchorPane and Delete it
- put a VBox on Content and set as StyleSheet the same IssueTrackingLite.css
- open the StyleClass menu ==> BUG it does not contain the expected 'darkList' and 'theme' rows (attached Emorej.fxml).

If you start with a blank document, put the VBox, set the same StyleSheet then the StyleClass menu's content is fine: it's really by taking the path described above the user comes into a dead end.