I've jused b42 to run this and it fails. When running from the IDE everything works as expected, packing up the stuff with the provided tooling it fails with an exception:

C:\e-ws\runtime-EclipseApplication\EfxclipseTest\deploy\dist>java -jar Efxclipse
Test.jar
05.09.2011 21:47:57 javafx.fxml.FXMLLoader logException
SCHWERWIEGEND: The following error occurred at line 15[Ljava.lang.StackTraceElem
ent;@2ce908
Exception in Application start method
java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.
java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at com.javafx.main.Main.launchApp(Main.java:354)
        at com.javafx.main.Main.main(Main.java:468)
Caused by: java.lang.RuntimeException: Exception in Application start method
        at com.sun.javafx.application.LauncherImpl.launchApplication1(Unknown So
urce)
        at com.sun.javafx.application.LauncherImpl.access$000(Unknown Source)
        at com.sun.javafx.application.LauncherImpl$1.run(Unknown Source)
        at java.lang.Thread.run(Thread.java:662)
Caused by: sun.misc.InvalidJarIndexException: Invalid index
        at sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:858)
        at sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:765)
        at sun.misc.URLClassPath.getResource(URLClassPath.java:169)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:194)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
        at sun.org.mozilla.javascript.internal.Kit.classOrNull(Kit.java:74)
        at sun.org.mozilla.javascript.internal.NativeJavaPackage.getPkgProperty(
NativeJavaPackage.java:140)
        at sun.org.mozilla.javascript.internal.NativeJavaPackage.get(NativeJavaP
ackage.java:91)
        at sun.org.mozilla.javascript.internal.ScriptableObject.getProperty(Scri
ptableObject.java:1301)
        at sun.org.mozilla.javascript.internal.ScriptRuntime.getObjectProp(Scrip
tRuntime.java:1326)
        at sun.org.mozilla.javascript.internal.ScriptRuntime.getObjectProp(Scrip
tRuntime.java:1315)
        at sun.org.mozilla.javascript.internal.Interpreter.interpretLoop(Interpr
eter.java:2804)
        at sun.org.mozilla.javascript.internal.Interpreter.interpret(Interpreter
.java:2239)
        at sun.org.mozilla.javascript.internal.InterpretedFunction.call(Interpre
tedFunction.java:138)
        at sun.org.mozilla.javascript.internal.ContextFactory.doTopCall(ContextF
actory.java:323)
        at sun.org.mozilla.javascript.internal.ScriptRuntime.doTopCall(ScriptRun
time.java:2747)
        at sun.org.mozilla.javascript.internal.InterpretedFunction.exec(Interpre
tedFunction.java:149)
        at sun.org.mozilla.javascript.internal.Context.evaluateReader(Context.ja
va:1169)
        at com.sun.script.javascript.RhinoScriptEngine.eval(RhinoScriptEngine.ja
va:106)
        at com.sun.script.javascript.RhinoScriptEngine.eval(RhinoScriptEngine.ja
va:124)
        at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:247)

        at javafx.fxml.FXMLLoader$ScriptElement.processEndElement(Unknown Source
)
        at javafx.fxml.FXMLLoader.processEndElement(Unknown Source)
        at javafx.fxml.FXMLLoader.load(Unknown Source)
        at layouttests.fxml.sample1.FXMLSample1.start(Unknown Source)
        at com.sun.javafx.application.LauncherImpl$5.run(Unknown Source)
        at com.sun.javafx.application.PlatformImpl$4.run(Unknown Source)
        at com.sun.javafx.application.PlatformImpl$3.run(Unknown Source)
        at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
        at com.sun.glass.ui.win.WinApplication.access$100(Unknown Source)
        at com.sun.glass.ui.win.WinApplication$2$1.run(Unknown Source)
        ... 1 more

The offending content is:
<fx:script>
  var USE_PREF_SIZE = Packages.javafx.scene.control.Control.USE_PREF_SIZE;
</fx:script>

when removed the fxml-File loads without problems. The fx-script was introduce because Greg Brown mentionned it in this blog post https://forums.oracle.com/forums/message.jspa?messageID=9842134#9842134