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that's really odd, and nothing much I could tell off hand.
I would recommend to
1) Try your queries in the dbxml shell - maybe you will get a better error, or nothing at all (the latter means that there is a problem in Java bindings)
2) Try to debug your application using gdb and see where the exception is thrown in C++ code (once I had to do this)
3) Try to narrow down the problem XQuery to a smaller XQuery
4) Try to execute an XQuery without importing modules or merge everything into one XQuery, just for testing (I remember there were some problems with XQuery library modules at some point)
Any further information would be useful to diagnose the problem