Sounds like a bug to me, too.
If you could distill your problem down to a test case, that would be
great. Or if you can just send us the whole schema, that would be fine
by me, too.
Also, try "-mode forest" option. This will make XJC dump all the inputs
it recognized along with their URIs. Probably you will find the same
schema listed twice under different URIs, and if you find them, send
please post those URIs (or send it to jaxb-comment_at_sun.com if you don't
want that to be public.)
Finally, the -use-runtime option is probably irrelevant for this problem.
--
Kohsuke Kawaguchi <kohsuke.kawaguchi_at_sun.com>