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Hm.  Are you *sure* that you are calling the close()
method?  I find it hard to believe that the stdio fclose()
wouldn't make the corresponding Win32 call to really close
the object. A fairly common failure mode in Python is to
have a local variable referencing an open file and assuming
that when the local variable goes out of scope, the file is
closed.  This will *usually* happen, but sometimes the stack
frame is kept alive (e.g. by exception handling machinery)
and that prevents the file from being closed.

I am very familiar with the Windows problem that you can't
remove/rename a file that's still open -- but I've never
heard of a case where making the explicit close() call
doesn't fix it.

Just trying to be helpful -- what you're embarking on seems
a big project...