R. David Murray added the comment:
Python doesn't know anything about X windows or window properties. (Well, it
might in tkinter, but meld appears to use GTK).
This is a bug in the meld application or one of the libraries it depends on,
not Python or its stdlib.
--
nosy: +r.david.mur
New submission from Yuri:
When I click on "Close Window" button for the unresponsive python-based app
'meld', message from window manager shows up offering to kill the non-existent
pid. It looks like python libs set wrong pid for windows when python
multithreading is in use by this app.
Here