all modules show up twice in the server console
Can you please elaborate? If you are seeing multiple log messages about the modules being deployed, post the same, lets see what the issue is. I am pretty much sure that the modules are NOT being deployed twice, because if it were to be the case then you would have seen exceptions related to JNDI naming of your EJBs and lot of other things.
Also, post the contents of your application.xml file.
I've created a totally simple web-application (packages inside an EAR) showing the problem, at least for JBoss 4.0.4.GA.
Here is the application.xml (created by Maven2):
<?xml version="1.0" encoding="UTF-8"?>
<application xmlns="http://java.sun.com/xml/ns/j2ee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/application_1_4.xsd" version="1.4">
I can attach the ready-to-deploy EAR, an image prooving that the WAR is showing up twice (actually three times if you count in the appearance under the EAR tree) and the source code of the two Eclipse projects used to create this testcase.
I can attach
It's just that I can't attach in this forum )-: