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Issue 1743 might be related to this.
Using "Save As..." in IDLE does work, but if breakpoints.lst is hidden 
(which it is when Python generates it) it also generates this error in 
the Shell:
Exception in Tkinter callback
Traceback (most recent call last):
 File "C:\Program Files\Python25\lib\lib-tk\Tkinter.py", line 1403, in 
__call__
 return self.func(*args)
 File "C:\Program Files\Python25\lib\idlelib\IOBinding.py", line 357, 
in save_as
 self.editwin.store_file_breaks()
 File "C:\Program Files\Python25\lib\idlelib\PyShell.py", line 209, in 
store_file_breaks
 new_file = open(self.breakpointPath,"w")
IOError: [Errno 13] Permission 
denied: 'C:\\Users\\Rich\\.idlerc\\breakpoints.lst'
The error is not generated if I manually unhide the breakpoints file.
The issue is unaffected by the hidden (or not) status of the .idlerc 
folder.