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Test this one out.If it doesn't work I need to look into it a bit more.
Oh, I don't think I have any control about the joint numbering. That's something which might have changed between different versions of the exporter from nemyax.
hmm.. generally, one wouldn't want stuff like joint numbering to change, but oh well.
I can't control it anyway
You probably can, to some extent. I don't do any sorting for child objects, and they appear in the order that Blender gives them to me. But I think you can influence that order by reparenting objects one by one.