Seems fx:deploy is unhappy if at least one of the JARs specified with fx:resources doesn't contain a MANIFEST.MF. Here's a stack trace:

path-to-build.xml:69: null
        at com.sun.javafx.tools.ant.DeployFXTask.execute(DeployFXTask.java:220)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:601)
        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.apache.tools.ant.Task.perform(Task.java:348)
        at org.apache.tools.ant.Target.execute(Target.java:390)
        at org.apache.tools.ant.Target.performTasks(Target.java:411)
        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
        at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
        at org.apache.tools.ant.Main.runBuild(Main.java:809)
        at org.apache.tools.ant.Main.startAnt(Main.java:217)
        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.lang.NullPointerException
        at com.sun.javafx.tools.packager.bundlers.BundleParams.getMainApplicationJar(BundleParams.java:390)
        at com.sun.javafx.tools.packager.bundlers.WinAppBundler.doValidate(WinAppBundler.java:59)
        at com.sun.javafx.tools.packager.bundlers.WinMsiBundler.validate(WinMsiBundler.java:90)
        at com.sun.javafx.tools.packager.bundlers.Bundler.get(Bundler.java:91)
        at com.sun.javafx.tools.packager.PackagerLib.generateNativeBundles(PackagerLib.java:450)
        at com.sun.javafx.tools.packager.PackagerLib.generateDeploymentPackages(PackagerLib.java:435)
        at com.sun.javafx.tools.ant.DeployFXTask.execute(DeployFXTask.java:215)
        ... 16 more

I ran into this when using JavaFX with Guice. One of the runtime dependencies is javax.inject (http://search.maven.org/remotecontent?filepath=javax/inject/javax.inject/1/javax.inject-1.jar) which happens to not have a manifest file.

Relevant OTN thread: https://forums.oracle.com/forums/thread.jspa?threadID=2425546