I took really long to reply for this post....
Nevertheless, we are successful in resolving the deployment issue with the help of IBM support
Though, they took nearly a month to identify the issue, finally they come up saying that there was EJB spec violations in the code which resulted in deployment failure. One of our application modules with MDBs had few jndi lookups performed in its constructor, as per the spec we cannot do this in a constructor. Because of this violation application didn't get deployed on WAS 6.1.0.15, however the same works fine on WAS 6.0 and WAS 6.1 with no EJB 3 feature pack. Since its not as per the spec, IBM doesn't guarantee their server behavior in such cases.
After removing jndi lookups from MDB's constructor application got deployed successfully.
Best regards,
Chandra.
[ August 26, 2008: Message edited by: Chandrasekhar Elindram ]