From John Hendrikx's mail:

I'm having trouble creating a reproducable test case.

There seems to be more going on -- if I open and close the Pane involved several times, eventually some of them will start to be GC'd (but never all, unless I disable the animation). I've used VisualVM to inspect the Pane involved, and here is what it says is keeping it alive (clearly something animation related atleast):

this - value: hs.mediasystem.screens.playback.PlaybackOverlayPane #1
<- this$0 - class: javafx.scene.Node$8, value: hs.mediasystem.screens.playback.PlaybackOverlayPane #1
<- target - class: com.sun.scenario.animation.shared.InterpolationInterval$DoubleInterpolationInterval, value: javafx.scene.Node$8 #149
<- [0] - class: com.sun.scenario.animation.shared.InterpolationInterval[], value: com.sun.scenario.animation.shared.InterpolationInterval$DoubleInterpolationInterval #28
<- [0] - class: com.sun.scenario.animation.shared.InterpolationInterval[][], value: com.sun.scenario.animation.shared.InterpolationInterval[] #10 (3 items)
<- interval - class: com.sun.scenario.animation.shared.GeneralClipInterpolator, value: com.sun.scenario.animation.shared.InterpolationInterval[][] #16 (1 items)
<- clipInterpolator - class: com.sun.scenario.animation.shared.TimelineClipCore, value: com.sun.scenario.animation.shared.GeneralClipInterpolator #16
<- clipCore - class: javafx.animation.Timeline, value: com.sun.scenario.animation.shared.TimelineClipCore #19
<- this$0 - class: javafx.animation.Animation$1, value: javafx.animation.Timeline #19
<- [5] - class: com.sun.scenario.animation.shared.PulseReceiver[], value: javafx.animation.Animation$1 #19
<- receivers - class: com.sun.javafx.tk.quantum.MasterTimer, value: com.sun.scenario.animation.shared.PulseReceiver[] #1 (7 items)
<- this$0 - class: com.sun.scenario.animation.AbstractMasterTimer$MainLoop, value: com.sun.javafx.tk.quantum.MasterTimer #1
<- animationRunnable - class: com.sun.javafx.tk.quantum.QuantumToolkit, value: com.sun.scenario.animation.AbstractMasterTimer$MainLoop #1
<- this$0 (JNI global) - class: com.sun.javafx.tk.quantum.QuantumToolkit$14, value: com.sun.javafx.tk.quantum.QuantumToolkit #1

If that is enough for a bugreport, I'll create one. A naive simple test case which spawns several panes and animations was unable to reproduce this issue I'm having:

package hs.mediasystem;

import javafx.animation.KeyFrame;
import javafx.animation.KeyValue;
import javafx.animation.Timeline;
import javafx.application.Application;
import javafx.application.Platform;
import javafx.beans.value.ChangeListener;
import javafx.beans.value.ObservableValue;
import javafx.beans.value.WeakChangeListener;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.layout.StackPane;
import javafx.stage.Stage;
import javafx.util.Duration;

public class TimelineGCProblem extends Application {

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

  @Override
  public void start(Stage stage) throws Exception {
    StackPane rootPane = new StackPane();
    Scene scene = new Scene(rootPane);

    stage.setScene(scene);
    stage.show();

    new Thread() {
      @Override
      public void run() {
        for(;;) {
          Platform.runLater(new Runnable() {
            @Override
            public void run() {
              rootPane.getChildren().setAll(new FadeInPane());
            }
          });

          try {
            System.gc();
            Thread.sleep(1500);
            System.gc();
          }
          catch(InterruptedException e) {
            e.printStackTrace();
          }
        }
      }

    }.start();
  }

  public static class FadeInPane extends StackPane {
    private final Timeline fadeInSustainAndFadeOut = new Timeline(
      new KeyFrame(Duration.seconds(0)),
      new KeyFrame(Duration.seconds(1), new KeyValue(opacityProperty(), 1.0)),
      new KeyFrame(Duration.seconds(6), new KeyValue(opacityProperty(), 1.0)),
      new KeyFrame(Duration.seconds(8), new KeyValue(opacityProperty(), 0.0))
    );

    private final ChangeListener<Scene> sceneChangeListener = new ChangeListener<Scene>() {
      @Override
      public void changed(ObservableValue<? extends Scene> observable, Scene oldValue, Scene newValue) {
        if(newValue != null) {
          System.out.println(">>> Starting fadeIn anim");
          fadeInSustainAndFadeOut.playFromStart();
        }
        else {
          System.out.println(">>> Stopping fadeIn anim");
          fadeInSustainAndFadeOut.stop();
        }
      }
    };

    public FadeInPane() {
      sceneProperty().addListener(new WeakChangeListener<>(sceneChangeListener));

      setStyle("background-color: red");
      getChildren().add(new Button("Hi"));
    }

    @Override
    protected void finalize() throws Throwable {
      super.finalize();
      System.out.println("FadeInPane finalized");
    }
  }
}