I had the same issue (although I'm using maven / javafx-maven-plugin; shouldn't make a difference). FX build tools signing seems broken at the moment, since as you noticed, jarsigner does not recognize the fact that the jar is signed, nor does the webstart launcher when running the deployed application.
I ended up signing my JavaFX application jars using a separate plugin (maven-jarsigner) in my build script.
I'd imagine you could use Ant's SignJar similarly.
See also this JavaFX JIRA issue, which is currently set to won't fix.