I found out the problem with our migration issue. It turns out that the migrate tool is depending on the dtd declaration to have the fully qualified url to the dtd. We had been using a local copy of the dtd file and thus had a relative path.
We had: <!DOCTYPE weblogic-ejb-jar PUBLIC "-//BEA Systems, Inc.//DTD WebLogic 8.1.0 EJB//EN" "/bea/weblogic81/server/lib/weblogic-ejb-jar.dtd">
Migrate tool expected: <!DOCTYPE weblogic-ejb-jar PUBLIC "-//BEA Systems, Inc.//DTD WebLogic 8.1.0 EJB//EN" "
http://www.bea.com/servers/wls810/dtd/weblogic-ejb-jar.dtd" >
We were expecting that since the dtd file name is the same, the path to the file would not impact the migration tool's ability to identify the file as a weblogic descriptor file.
[Message sent by forum member 'jtveita' (jtveita)]
http://forums.java.net/jive/thread.jspa?messageID=283363