The error I kept on getting was java.lang.IllegalStateException: Internal error - type definition not found. With verbose output enabled, this is what JiBX CodeGen output...
After some research, I found a post that pretty much described the issue that I was seeing. Unfortunately I could not find any ways around this without having to spend a significant effort to modify the schema.
Expanding on the post I found, this is what the schema layout looks like (arrows show import or include). I created this image using twopi and dotty tools from Graph Viz.
The circular dependencies are quite clear.
The only schema that I could successfully generate bindings for was NarrativeBlock.xsd, this is because it's a leaf node in the overall schema layout without any other includes/imports. Every single other XSD failed with the same exception.
It's a shame that JiBX can't handle this kind of schema layout, but then the HL7/CDA schema is not the best example of good schema design either.