Personal I'm using Scene Builder 2.0 to do the layout of my JavaFX application. When I see the application through Scene Builder everything is ok, but when I run the JavaFX application the side is not the same as the Scene Builder drawing, it has a bigger space on the right side, I attached a print of each one for you to see the difference . The first is the image of the application, the second of the Scene Builder
<?xmlversion="1.0" encoding="UTF-8"?>
<?import javafx.geometry.*?>
<?import java.lang.*?>
<?import java.util.*?>
<?import javafx.scene.*?>
<?import javafx.scene.control.*?>
<?import javafx.scene.layout.*?>
<TabPane fx:id="tabPane" prefHeight="558.0" prefWidth="628.0" tabClosingPolicy="UNAVAILABLE" xmlns="http://javafx.com/javafx/8" xmlns:fx="http://javafx.com/fxml/1" fx:controller="br.com.grupor.controlepostal.viewController.CadastroDestinatarioViewController">
<tabs>
<Tab fx:id="tabLista" text="Destinatários">
<content>
<FlowPane prefHeight="506.0" prefWidth="618.0">
<children>
<Label contentDisplay="CENTER" text="Filtrar Destinatário">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Label>
<TextField fx:id="textFiltrarDestinatario" onKeyReleased="#filtrarDestinatarioOnReleased" prefHeight="25.0" prefWidth="510.0">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</TextField>
<Label text="Destinatários Localizados">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Label>
<ComboBox fx:id="comboBoxLocalizados" prefHeight="25.0" prefWidth="473.0">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" top="5.0" />
</FlowPane.margin>
</ComboBox>
<FlowPane alignment="CENTER_RIGHT" prefHeight="35.0" prefWidth="624.0">
<children>
<Button fx:id="btnNovo" mnemonicParsing="false" onAction="#btnNovoOnAction" text="Novo">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Button>
<Button fx:id="btnAlterar" mnemonicParsing="false" onAction="#btnAlterarOnAction" text="Alterar">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Button>
<Button fx:id="btnExcluir" mnemonicParsing="false" onAction="#btnExcluirOnAction" text="Excluir">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Button>
</children>
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</FlowPane>
<TableView fx:id="tableViewLista" onMouseClicked="#tableViewListaClicked" prefHeight="404.0" prefWidth="619.0">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</TableView>
</children>
</FlowPane>
</content>
</Tab>
<Tab fx:id="tabCadastro" text="Cadastro">
<content>
<FlowPane prefHeight="529.0" prefWidth="592.0">
<children>
<Label text="Destinatário">
<padding>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</padding>
</Label>
<TextField fx:id="textDestinatario" prefHeight="27.0" prefWidth="547.0">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</TextField>
<ComboBox fx:id="comboBoxTipoPessoa" prefWidth="150.0">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</ComboBox>
<Label text="Documento">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Label>
<TextField fx:id="textDocumento">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</TextField>
<Label text="OBS">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Label>
<TextField fx:id="textObs" prefHeight="25.0" prefWidth="196.0">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</TextField>
<Label text="CEP">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Label>
<TextField fx:id="textCep" prefHeight="25.0" prefWidth="75.0" />
<Label text="Endereço">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Label>
<TextField fx:id="textEndereco" prefHeight="25.0" prefWidth="455.0">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</TextField>
<Label text="Complemento">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Label>
<TextField fx:id="textComplemento" prefHeight="25.0" prefWidth="214.0">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</TextField>
<Label text="Bairro">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Label>
<TextField fx:id="textBairro" prefHeight="25.0" prefWidth="269.0">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</TextField>
<Label text="Cidade">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Label>
<TextField fx:id="textCidade" prefHeight="25.0" prefWidth="482.0">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</TextField>
<Label text="Estado">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Label>
<TextField fx:id="textEstado" prefHeight="25.0" prefWidth="36.0">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</TextField>
<Label text="E-mail">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Label>
<TextField fx:id="textEmail" prefHeight="25.0" prefWidth="330.0">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</TextField>
<Label text="Contato">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Label>
<TextField fx:id="textContato" prefHeight="25.0" prefWidth="184.0">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</TextField>
<FlowPane alignment="TOP_RIGHT" prefHeight="35.0" prefWidth="631.0">
<children>
<Button fx:id="btnCancelar" mnemonicParsing="false" onAction="#btnCancelarOnAction" text="Cancelar">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Button>
<Button fx:id="btnSalvar" mnemonicParsing="false" onAction="#btnSalvarOnAction" text="Salvar">
<FlowPane.margin>
<Insets bottom="5.0" left="5.0" right="5.0" top="5.0" />
</FlowPane.margin>
</Button>
</children>
<FlowPane.margin>
<Insets />
</FlowPane.margin>
</FlowPane>
</children>
</FlowPane>
</content>
</Tab>
</tabs>
</TabPane>