IIRC, GW included the NYGM Ship damage mod. Major changes were made to this including removal of stock SH3 magic kill areas. there has been a lot of discussion about this, if you haven't followed along with them or have not read the in depth read me of the damage mod and how it has been altered try this topic and also get the read me from the d/l link.
http://www.subsim.com/phpBB/viewtopi...highlight=nygm