It looks like this is due to the order of methods returned by Class.getDeclaredMethods().

In PropertyContainer.java, if I change lines 182-3 from

		List<XProperty> properties = xClass.getDeclaredProperties( access.getType() );
		for ( XProperty property : properties ) {

to

		List<XProperty> properties = xClass.getDeclaredProperties( access.getType() );
		Collections.reverse( properties );
		for ( XProperty property : properties ) {

then the test passes.

Perhaps the root problem is that JavaXClass.getDeclaredMethodProperties() returns two properties for TheEntity (one for isId() and one for getId()); it should probably be smart enough to ignore the isId() one.