Please report in jira with steps to how to reproduce (i.e. the above description is not enough since you don't say what kind of project it is, how you created it and how you are deploying it...)
Are you including already bundled jar files directly in your ear project or are you setting them up as separate utility projects?
Created jira report at https://jira.jboss.org/jira/browse/JBIDE-4676.
Each utility project is a separate Eclipse project; MyMDB and MyEar are a separate Eclipse projects as well. Each utility project is set to go into the "lib" directory in the EAR configuration.
I'm not using maven, so I didn't have any of the project setup (facet installation) issues, but the /lib directory not being populated sounds exactly the same :P
While I was walking through the steps to reproduce the issue, I noticed that different behavior was exhibited depending on the server type I was using. If I used the "JBoss v5.0" server (under the "JBoss" group), it build a compressed .ear with the /lib directory missing. If I used the "JBoss AS 5.1" server (under the "JBoss Community" group), then it build an exploded EAR with the Utility1.jar under the root. I am not too familiar with exploded deployments, but I would expect the Utility1.jar file to appear under the MyEar.ear/lib directory. Does that sound correct?
Thanks for the help!