I have done some investigations, and I'm quite sure that:
1. Oracle forgot to update the certificate in January (we all know that).
2. Oracle updated the certificate to one that's expiring 2014 instead of January 2012 (I have gotten the new certificate).
3. Somehow, things got reverted recently to the old expired certificate again (Now you will get the old certificate again).
I have written more detailed about this in: javafx-rt.jnlp links to corrupted JARs
Still haven't found the newly signed runtime files myself, but wanted to share my workaround:
If you are signing your app, adding the JavaFX runtime jars to javafx packager -classpath list signs the jars with your cert.
Just make sure you copy the newly signed runtime jars back into the javafx-runtime dir and you shouldn't have to make any changes to the javafx-rt.jnlp