There is some info here:

http://wiki.jboss.org/wiki/Wiki.jsp?page=ClassLoadingConfiguration

I don't have much experience in this since I haven't had that many classloading 
problems but following seam-gen example, try putting in the ear META-INF a 
jboss-app.xml with


  | <?xml version="1.0" encoding="ISO-8859-1"?>
  | <!DOCTYPE jboss-app
  |     PUBLIC "-//JBoss//DTD J2EE Application 4.2//EN"
  |     "http://www.jboss.org/j2ee/dtd/jboss-app_4_2.dtd";>
  | 
  | <jboss-app>
  |     <loader-repository>seam.jboss.org:loader=unique</loader-repository>
  | </jboss-app>
  | 

and something other unique in the other ear.

It's a long shot since one would think that normally one ear couldn't possible 
have effect on the other but experience shows otherwise as you have 
experienced...

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