The ClassPathJaxb2TypeScanner class is a helper class for Jaxb2Marshaller that scans given packages for classes marked with JAXB2 annotations. However, it does not scan for the @XmlRegistry annotation, which is used on ObjectFactory classes.
In some cases, the ObjectFactory classes contain crucial annotations for JAXB such as the following:
Without have scanned these annotations, JAXB will not recognize "myElement" as a valid substitution for "myBaseElement" and unmarshalling will fail.
I have attached a very simple maven project with two test cases which illustrates the issue (pure JAXB).
The resolution of the issue is simple (I have also tested this in the project where we ran into the problem). All that is necessary is to add XmlRegistry to the list of scanned annotations in ClassPathJaxb2TypeScanner, i.e.: