Maybe only a linux related bug, try this and you should see that instead of being centered, the text starts at the center of the TextField.
I don't know if Platform.runLater() is mandatory for setText but it doesn't change anything to use it or not.

package test;

import javafx.application.Application;
import javafx.application.Platform;
import javafx.geometry.Pos;
import javafx.scene.Scene;
import javafx.scene.control.TextField;
import javafx.scene.layout.BorderPane;
import javafx.stage.Stage;

public class Test extends Application {

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

@Override
public void start(Stage stage) throws Exception {
BorderPane bp = new BorderPane();
final TextField tf = new TextField();
tf.setAlignment(Pos.CENTER);
tf.setPrefColumnCount(20);
tf.setMaxHeight(20);
tf.setMaxWidth(200);
bp.setCenter(tf);
Scene scene = new Scene(bp, 300, 300);
stage.setScene(scene);
stage.show();
new Thread(new Runnable() {

@Override
public void run() {
try {
Thread.sleep(3000);
} catch (InterruptedException e) {
}
// tf.setText("try to center this !"); -- same behavior as with
// Platform.runLater()
Platform.runLater(new Runnable() {

@Override
public void run() {
tf.setText("try to center this !");
}

});
}
}).start();
}
}