This is a bit hard to answer without seeing the whole compilation. However I often got this error when compiling third-party schemas in the case when the same schema was included via different URLs.
I.e. I've implemented a project which compiled an extensive set of OGC Schemas. The problem was that these schemas referenced each other via relative and absolute URLs. So when I customized one of the schemas there were other schemas for the same namespace URI. Since JAXB processes imports and includes, it is not quite transparent what exactly gets compiled. Try to check your XJC logs for cues or - if you compile schemas directly via URLs (which is not recommended) - go through a logging proxy and see what actually gets accessed.