Thanks for the links and help.
But I did slightly lie, I am running SUN AS 9 not glassfish.
But now I have another problem. As soon as I add another cert to the keystore the domain won't start. If I remove the added cert it will start up.
Rather than fight this problem we are just going to create a seperate keystore for the application to use.
[Message sent by forum member 'bryanut' (bryanut)]
http://forums.java.net/jive/thread.jspa?messageID=316581