About a week ago Nate, announced he fixed a bug which effects IK which manipulate a single bone (not two bones) when flipped. However, this bug still occurs in unity if you flip the skeleton:
My reply in the thread viewtopic.php?f=7&t=3854
"Hi,
I just checked it with unity (using the latest runtime) and the problem still persists. When an IK is manipulating two bones and the X is flipped it works fine, but if the IK is manipulating one bone then it does not resolve correctly. Is there something special that needs to be called?
Its also worth noting it happens in editor too.
"
I am aware there are work arounds, but these work arounds have a lot of repercussions. Hopefully this will be fixed soon.