I've checked again the source code in config_key.py, configdialog.py, help_about.py, query.py, searchbase.py, textview.py and added a self.grab_release() in functions like ok() and cancel() before the call to self.destroy() and I see no more lock/focus issues. Maybe the grab was kept in the non-existent (destroyed) dialog window, so the click events could not be transferred to the pyshell or editor, but, because of a local (not global) grab, clicking on another application's window, by losing focus and grab, completely freed the event-chain, then clicks in IDLE were correctly received.
Can you confirm if adding the grab_release() calls works for you too (do not remove the grab_set() calls!)?