I had this bug a few days ago, I was upgrading from etch to lenny.
I found a solution, you will find my solution on my blog[1].
But that problem caused stopping of the upgrade, during upgrade, a
problem like this one shouldn't stop the upgrade, aptitude/apt should
upgrade the rest of packages that are not yet upgraded, because
module-init-tools is before them.
This "patch"[2] didn't solve the problem. (even if the bash code seems
to do the same things I did in my solution...)
[1] :
http://en.about-gnulinux.info/index.php?post/2009/02/14/The-package-module-init-tools-causes-problem...
[2] : http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=509575#25
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