ADDITIONAL SYSTEM INFORMATION :
openjdk 11.0.15
Problem shows up on both JavaFX 11 and JavaFX 18.0.2
Problem shows up on CentOS 7 and RHEL 7. Does not show up on Windows 10.
Currently testing on the following graphics card with the proprietary nvidia drivers, although it shows up with other nvidia cards:
Graphics Vendor: NVIDIA Corporation
       Renderer: Quadro GP100/PCIe/SSE2
        Version: 4.6.0 NVIDIA 515.57

A DESCRIPTION OF THE PROBLEM :
The pulse loop waits for one vsync per a dirty scene. If I have multiple windows open, each with their own scene, and each scene is continuously updating (always dirty), the frame rate is 60 fps / number of windows.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Create an application with multiple stages and update the contents of each stage every call to an `AnimationTimer` (make each stage constantly dirty).

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Smooth, 60 frames per second animations. Adding multiple windows with simple contents should not increase the time it takes until the next pulse.
ACTUAL -
Frame rate is 60 frames per second *divided by the number of windows*. Adding multiple windows with simple, but animated contents significantly decreases the frame rate.

---------- BEGIN SOURCE ----------
package multiplescenes;

import javafx.animation.AnimationTimer;
import javafx.application.Application;
import javafx.beans.binding.Bindings;
import javafx.beans.property.DoubleProperty;
import javafx.beans.property.LongProperty;
import javafx.beans.property.SimpleDoubleProperty;
import javafx.beans.property.SimpleLongProperty;
import javafx.beans.value.ObservableDoubleValue;
import javafx.beans.value.ObservableLongValue;
import javafx.scene.Scene;
import javafx.scene.control.Label;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class MultipleDirtyScenes extends Application {
    private static final int SCENE_COUNT = 3;

    @Override
    public void start(Stage ignorePrimaryStage) {
        final FramesPerSecondCounter frameRateCounter = new FramesPerSecondCounter();
        frameRateCounter.start();

        for (int i = 0; i < SCENE_COUNT; i++) {

            final Label fpsLabel = new Label();
            fpsLabel.textProperty().bind(Bindings.format("FPS: %.1f", frameRateCounter.fpsProperty())); // FPS will be ~ 60.0/SCENE_COUNT
            final Label lastFrameTimeNsLabel = new Label();
            lastFrameTimeNsLabel.textProperty().bind(Bindings.format("Last frame time (ns): %d", frameRateCounter.lastFrameTimeNsProperty())); // Makes the scene constantly dirty

            final Scene scene = new Scene(new VBox(fpsLabel, lastFrameTimeNsLabel), 480, 100);

            final Stage stage = new Stage();
            stage.setScene(scene);
            stage.show();
        }
    }

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

    private static class FramesPerSecondCounter extends AnimationTimer {

        private static final int FRAME_TIME_COUNT = 10;
        private final long[] frameTimesNs = new long[FRAME_TIME_COUNT];
        private int frameTimeIndex = 0;
        private final LongProperty lastFrameTimeNs = new SimpleLongProperty();
        private final DoubleProperty fpsValue = new SimpleDoubleProperty();

        @Override
        public void handle(final long nowNs) {
            lastFrameTimeNs.set(nowNs);

            final long oldFrameTimeNs = frameTimesNs[frameTimeIndex];
            frameTimesNs[frameTimeIndex] = nowNs;
            frameTimeIndex = (frameTimeIndex + 1) % frameTimesNs.length;

            final long elapsedNanos = nowNs - oldFrameTimeNs;
            final long elapsedNanosPerFrame = elapsedNanos / frameTimesNs.length;
            final double fps = 1_000_000_000.0 / elapsedNanosPerFrame;
            fpsValue.set(fps);
        }

        public ObservableDoubleValue fpsProperty() {
            return fpsValue;
        }

        public ObservableLongValue lastFrameTimeNsProperty() {
            return lastFrameTimeNs;
        }
    }
}
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Use *both* `-Dprism.vsync=false` and environment variable `__GL_SYNC_TO_VBLANK=0` (see https://bugs.openjdk.org/browse/JDK-8168366).

FREQUENCY : always