I know it's probably really silly problem and easily fixable but I'm really new in rigging. I Try to mirror skeleton to the other side. I use Mirror Hierarchy X and it gives me...

Joints are also flipped in Z axis. The third joint shows exactly the issue. Any solutions ?
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That said... I'm trying to replicate the issue here to see if I can figure out what I do to fix it... and of course that means it's decided to work 100% perfectly.
Can you upload an lxo with the half you're trying to mirror over?
Here is the file: LINK
I'm in Setup tab, selecting the root bone of the hierarchy and clicking Mirror Hierarchy X...
Here's the mirrored version...
http://www.speedyshare.com/W9rNP/dude-rigging.lxo
Well Modo must sometimes be a drama queen...