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Sometimes things like this can be a real pain to debug. I have gotten so used to reimaging my machine that if it takes more than 10 minutes...I use the asr tool to reimage my Operating System from an image I keep on a second partition.
I have my User's folder symbolically linked to the second hard drive so I can easily erase my main partition by booting into the second partition.
I have some example code that is more geared toward doing this from a netboot image, but you could implement this on a second partition:
http://smartosxdeploy.googlecode.com/svn/trunk/nuke.py
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