Standard Java properties operate under the principal of "first come first served". Once a property has a value it is not changed by a later attempt.

The method org.hibernate.cfg.Configuration.addProperties(Element parent) should read

private void addProperties(Element parent) {
Iterator iter = parent.elementIterator( "property" );
while ( iter.hasNext() ) {
Element node = (Element) iter.next();
String name = node.attributeValue( "name" );
String value = node.getText().trim();
log.debug( name + "=" + value );
if (properties.containsKey(name)
continue;
properties.setProperty( name, value );
if ( !name.startsWith( "hibernate" ) ) {
properties.setProperty( "hibernate." + name, value );
}
}
Environment.verifyProperties( properties );
}