The methods afer() and after_idle() register the
callback function in the list self._tclCommands. This
List is member of the Misc class in the file tkinter.py
and is not protected by a lock. 
So it could be that the thread  access the list by
calling the function after() and to the same time the
tkinter mainloop access the list  by the methode
deletecommand() in the callback function.  The same
problem will occur if the function after() is called by
two theads.

solution: 
Create a lock object and save the list 
self._tclCommands in the methods :

misc.destroy()
misc.deletecommand()
misc._register()

This is not going to happen.
You should be protecting it yourself since this is a special case.