My fx:jar task looks like this:
<fx:jar destfile="${application.dist}/${application.jarfile}-${project.version}.jar">
<fx:application refid="MyApp" />

<manifest>
<attribute name="Class-Path" value="${manifest.classpath}" />
<attribute name="Specification-Version" value="${project.version}" />
<attribute name="Implementation-Version" value="${project.version}" />
</manifest>

<!-- The target/classes folder which contains all resources and class files -->
<fileset dir="${project.build.outputDirectory}" />
</fx:jar>

When building with any released version of Java this generates a correct MANIFEST.MF in the resulting jar file, with the class-path element as I specified it. However, when I switch my JAVA_HOME to jdk1.7.0_12 with the 2.2.6-ea JavaFX version (still the latest released early access version right?) the resulting jar doesn't contain the class-path element. So when I double click the jar I get an error (because the classpath isn't specified), the jar build with 7.0.17 starts perfectly.
I tried removing the <manifest> element completely from my build.xml but that didn't change anything. Since this jar is then also used by the fx:deploy task, this results in non working native builds.