The fix turned out to be fairly involved too – on the order of a week I think.
Ivan works from Bulgaria so sadly he is asleep right now.
Usually the stack trace when a NoClassDefFoundError is thrown contains a "Cause" clearly showing the name of the class loader that was supposed to know about the class in question, and which then rather obviously failed to load it. If it actually isn't in the real trace, the exception/error logging is probably a bit wonky.
I have seen logging procedures that don't traverse/print the entire traceback chain, but only prints the message and the immediate stack. But this is unfortunately a rather terrible idea. Quite often it will exclude the actual cause from the printed trace while simulataneously retaining the error message, not rarely leading to liberal amounts of confusion. The pattern with exceptions being thrown with a cause is not uncommon in the JDK, so making sure to log causes are important.
In general, although it's probably obvious, I would like to mention that having code loaded by class loaders with different lifetimes interact is rife with "interesting" issues. Wherever possible I would recommend serializing messages over any boundaries where class loaders have different lifetimes, as it both prevents all of the strangest causes of errors, and can also lead to a cleaner design. An exception would be if prohibitively expensive from a performance perspective, of course.