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Double check your jar file. Are you sure the stylesheet is in there and where you expect it to be?
This was caused by the way I was initializing the FXML loader instance. When I changed to how the examples were doing it by specifying the full path to the fxml file when creating the loader instance, it worked fine with the relative urls.
For example FXMLLoader loader = new FXMLLoader("full/path/to/fxml");