Creating a PopupControl with a child that overrides getUserAgentStylesheet generates some warnings:

Mar 19, 2014 2:27:21 PM javafx.scene.CssStyleHelper calculateValue
WARNING: Could not resolve '-fx-text-background-color' while resolving lookups for '-fx-text-fill' from rule '*.label' in stylesheet jar:file:/Library/Java/JavaVirtualMachines/jdk1.8.0.jdk/Contents/Home/jre/lib/ext/jfxrt.jar!/com/sun/javafx/scene/control/skin/modena/modena.bss
Mar 19, 2014 2:27:21 PM javafx.scene.CssStyleHelper calculateValue
WARNING: Could not resolve '-fx-text-background-color' while resolving lookups for '-fx-text-fill' from rule '*.label' in stylesheet jar:file:/Library/Java/JavaVirtualMachines/jdk1.8.0.jdk/Contents/Home/jre/lib/ext/jfxrt.jar!/com/sun/javafx/scene/control/skin/modena/modena.bss
Mar 19, 2014 2:27:21 PM javafx.scene.CssStyleHelper calculateValue
WARNING: Could not resolve '-fx-text-background-color' while resolving lookups for '-fx-text-fill' from rule '*.label' in stylesheet jar:file:/Library/Java/JavaVirtualMachines/jdk1.8.0.jdk/Contents/Home/jre/lib/ext/jfxrt.jar!/com/sun/javafx/scene/control/skin/modena/modena.bss
Mar 19, 2014 2:27:21 PM javafx.scene.CssStyleHelper calculateValue
WARNING: Could not resolve '-fx-text-background-color' while resolving lookups for '-fx-text-fill' from rule '*.label' in stylesheet jar:file:/Library/Java/JavaVirtualMachines/jdk1.8.0.jdk/Contents/Home/jre/lib/ext/jfxrt.jar!/com/sun/javafx/scene/control/skin/modena/modena.bss

But instead of overriding getUserAgentStylesheet, simply loading the css file in the constructor works fine (see sample demo below)

[Demo.java]
import javafx.application.Application;
import javafx.event.ActionEvent;
import javafx.scene.Node;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.Control;
import javafx.scene.control.Label;
import javafx.scene.control.PopupControl;
import javafx.scene.control.Skin;
import javafx.scene.layout.Pane;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class Demo extends Application {
    class MyCustomControl extends Control {
        class MyCustomControlSkin implements Skin<MyCustomControl> {
            private final MyCustomControl customControl;
            private final Pane node;
            public MyCustomControlSkin(final MyCustomControl control) {
                this.customControl = control;
                this.node = new Pane(new Label("Custom control"));
                //getStylesheets().add(MyCustomControl.class.getResource("mycustomcontrol.css").toExternalForm());
            }
            @Override public MyCustomControl getSkinnable() {
                return customControl;
            }
            @Override public Node getNode() {
                return node;
            }
            @Override public void dispose() {}
        }
        
        public MyCustomControl() {
            getStyleClass().add("my-custom-control");
        }
        @Override protected Skin<?> createDefaultSkin() {
            return new MyCustomControlSkin(this);
        }
        @Override public String getUserAgentStylesheet() {
            return MyCustomControl.class.getResource("mycustomcontrol.css").toExternalForm();
        }
    }
    
    class MyPopupControlSkin implements Skin<PopupControl> {
        private final PopupControl popupControl;
        private final Pane node;
        public MyPopupControlSkin(final PopupControl control) {
            this.popupControl = control;
            this.node = new VBox(new Label("Popup control"), new MyCustomControl());
        }
        @Override public PopupControl getSkinnable() {
            return popupControl;
        }
        @Override public Node getNode() {
            return node;
        }
        @Override public void dispose() {}
    }
    
    @Override public void start(Stage primaryStage) {
        Button btn = new Button("Open popup");
        btn.setOnAction((ActionEvent e) -> {
            PopupControl popup = new PopupControl();
            popup.setSkin(new MyPopupControlSkin(popup));
            popup.show(btn, primaryStage.getX() + 160, primaryStage.getY() + 30);
        });
        primaryStage.setScene(new Scene(btn, 150, 50));
        primaryStage.show();
    }

    public static void main(String[] args) {
        launch(args);
    }
}

[mycustomcontrol.css]
.my-custom-control {
    -fx-background-color: yellow;
}