I get the same problem when I try to change the key set.  This is on on 
intel build using Tk 8.5, and the latest 3.1 source checked out with 
bzr.  

I too changed the order of /Library/Frameworks and 
/System/Library/Frameworks in setup.py

A simple fix for me was to add the line

root.instance_dict = {}

in macosxsupport.py  That does not seem to have any other ill effects.