Make difference between empty and bone axis
Please, I spend the last 3 hours trying to debug what is going on. I tough it was empty in the scene and brake the whole rig to get to it and it was Axis checked on on one of the rig bones. Consider changing at least colors when "Axis" is turned on at bones.
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You can make the color of the unselected Empty different in the theme tab. Not the same, but solves the problem.