Calling setWidth() or setHeight() method for each stage I have created at the same time, some stages aren't resized as expected. Adding a change listener to relative properties (widthProperty or heightProperty) you can see the value is changed correctly, but the stage isn't resized. With several stages (15, 20 or more) this behavior is more frequent.
I noticed this behavior using java 1.8.0-b132.

Test code:

import javafx.beans.value.ChangeListener;
import javafx.beans.value.ObservableValue;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.layout.StackPane;
import javafx.stage.Stage;

public class Application extends javafx.application.Application {

@Override
public void start(final Stage primaryStage) {
final ObservableList<Stage> stages = FXCollections
.observableArrayList();

// Number of stages to create
int count = 20;
int columns = 5;

int curColumn = 1;
for (int i = 0; i < count; i++) {
if (i % columns == 0) {
curColumn++;
}
final Stage stage = new Stage();
stage.setTitle("Stage " + (i + 1));
stage.widthProperty().addListener(new ChangeListener<Number>() {
@Override
public void changed(ObservableValue<? extends Number> obs,
Number oldX, Number newX) {
System.out.println(stage.getTitle() + " W changed from "
+ oldX + " to " + newX);
}
});

Button btn = new Button("Resize");
btn.setOnAction(new EventHandler<ActionEvent>() {
@Override
public void handle(ActionEvent arg0) {
System.out.println("\nResizing");
for (Stage stg : stages) {
stg.setWidth(150.0);
}
}
});
stage.setScene(new Scene(new StackPane(btn)));
stage.setWidth(200.0);
stage.setHeight(60.0);
stage.setX(50 + 200.0 * (i % columns));
stage.setY(70 * curColumn);
stage.show();
stages.add(stage);
}
}

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