I upgraded to JavaMail 1.4.7 in App 1 which didnt fix the issue as suggested on other posts. I did programmatically set the MailcapCommandMap config as per below which worked. Note this was taken from another post.
MailcapCommandMap mailcapCommandMap = (MailcapCommandMap) CommandMap.getDefaultCommandMap();
mailcapCommandMap.addMailcap("text/html;; x-java-content-handler=com.sun.mail.handlers.text_html");
mailcapCommandMap.addMailcap("text/xml;; x-java-content-handler=com.sun.mail.handlers.text_xml");
mailcapCommandMap.addMailcap("text/plain;; x-java-content-handler=com.sun.mail.handlers.text_plain");
mailcapCommandMap.addMailcap("multipart/*;; x-java-content-handler=com.sun.mail.handlers.multipart_mixed");
mailcapCommandMap.addMailcap("message/rfc822;; x-java-content-handler=com.sun.mail.handlers.message_rfc822");
CommandMap.setDefaultCommandMap(mailcapCommandMap);