I am assuming you are deploying two distinct web apps with each of them having pus with same name and pointing to same data source.
You seem to be using an older version of EclipseLink which AFAIR was not robust enough to handle this situation. Try running with a newer version of EclipseLink or if that is not an option, change pu name for one of the apps.
[Message sent by forum member 'mm110999']
http://forums.java.net/jive/thread.jspa?messageID=473233