Thanks Wolf-Dieter Fink.
That has fixed the problem. I hadn't thought that although Emacs saw the XML as valid the DTD might have an order to the tags.
I also had a problem with the MySQLInnoDialect not working because of a typo and I should have been using "MySQL5InnoDBDialect".
Just for anyone coming a long afterwards there is also two problems with the EJB file:
1). The setUUID(String newUUID) should, of course, be called "setIdentity(String new UUID)" or the parsing of the EJB will fail because hybernate will fail as it can't find a setter for the key.
2). The getUUID() method needs to be marked as "@Transient" so that hybernate doesn't try to map it to a database object.
But with these three little change my test EJB gets deployed and the table created in the database. I'm now a happy bunny.
Many thanks