Hi Greg,
I can’t reproduce the problem [assuming you are on R19]. Have you tried to create a new rig, and get the same results each time?
Normally the scene file would be required, as from an screenshot I can’t tell what happens. So I tired many times, setting up a new rig and deleting one side of weights to see how the results arrive After “Mirror - to+ ” or “Mirror + to -”
The Hierarchy how it was during Binding will be stored inside of the Weight. Any change later on in the Object Manger, will be not reflected. So, it seems that hierarchy problem started before the Binding, and hence any operation after that will perhaps not work well, even if the Object Manager content will receive a fix of the Hierarchy.
Given that the hierarchy was not the same, the problems are a logical result.
In anyway, I had the same results, no re-organization of the hierarchy based on switching the “Joint Filter” options. In your screenshot the hierarchy itself has changed, so I’m not even sure if the weight is copied wrongly, as the change of hierarchy as shown might not be the problem. Hence the question, have you tired to do it again. So without more information, there is nothing that I can do here.
With that being said, please contact the support:
https://www.maxon.net/en-us/support/how-can-we-help/
My best wishes