I am new in this forum, so may be you already found a solution to your problem ...
What I can say you is that to deploy a web application under JBoss, you have to put it under:
It is for my instalation, in fact aou have to put it under "YOUR_JBOSS_HOME\server\default\deploy" directory if you use the default server ...
Jboss does not take into account what you put under TOMCAT ....
You have just to rename the directory you put under TOMCAT,
e.g. if the name was TUTU, then you have to rename it TUTU.war, or if it is an archive, you can extract it and put all in such a directory, or to create a jar file and to rename it as a .war
i can get "basic" war files to deploy by putting the myapp.war file in the dir: /opt/jboss/server/default/deploy
But I have an application with "complicated" library paths (read by Servlets) set in ./WEB-INF/web.xml in the war file, and these settings aren't read correctly by jboss-3.0.4_tomcat-4.1.12. I get it to work by extracting the war file to /opt/jboss/server/deploy/myapp.war DIRECTORY.