Deepak,
I don't think there is a reason to panic. From an
EJB 3 perspective, JBoss 4.2 is very good functionally. Truth be told, JBoss has always been a little lax from a compliance standpoint. However, that is only one metric to a sucessful application server. Also, as I stated earlier, it is almost imposible to be 100% spec compliant. The important thing is that your code is spec compliant and therefore portable.
As to Java EE 5 certification, every major vendor is now certified, including JBoss 5, GlassFish, WebLogic 10, Geronimo and WebSphere 7.
Best regards,
Reza