Did you ever get an answer to this? I am having the same problem.
My DOCTYPE tag didn't have everything that it needed. It required that the DOCTYPE have the "-//Sun Microsystems, Inc.//DTD J2EE Application 1.3//EN" clause. It specificaly checks the file to see if this is there and returns null if it is not.
Sorry to ask but just have to check, you type META-INT/application.xml, this was a type in your post not your ear?