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Looking at your example code (as best I can guess about 
indentation), it looks like

module x <==> class X
module x <==> class A ==> A's instance x ==> class X
module x <==> class B ==> B's instance x ==> class X

So the x instances can't go away until A and B do, which 
means at module cleanup.  But when the module cleans up, it 
may well clean up X before A, so that A.x no longer has an 
active class, so that it can't find its __del__ method.