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The funny interaction with modules is probably that the 
module retains a reference to the class (and vice versa), 
so the class can't go away until the module does -- and a 
module in sys.modules can't go away.

The __del__ methods are not called if the interpreter can't 
decide which to call first.  For example, if

    A.attr=B
    B.attr=A

then A and B form a cycle (like the class and its defining 
module).  If only one has a __del__ method, it gets called, 
but if both do, then python doesn't know which to call 
first, so it never calls either.

You may have a cycle like

module <==> class <==>instanceA
               \  <==>instanceB

So that it can't decide whether to take care of instanceA 
or instanceB first.

Or it might be that the __del__ methods actually are being 
called, but not until module teardown has begun, so they 
don't work right.