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This turned about to be a java classloader issue like explained on https://groups.google.com/forum/?fromgroups=#!topic/android-ndk/2gkr1mXKn_E. The solution is to cache all needed jclass instances as global refs, and then use those global refs from the callback thread.
I suspect a better solution is to provide a 'root' which would either be a class loader or even a class. And that is accessible from a java global context.
Your JNI gets the root and from that is can get the class loader.