This may not be related but I wanted to share my experiences nevertheless. I had some problems upgrading my tetex installation. The script would complain about references to an old texmf tree while the new (for 3.x) would be ~/.texmf/. This happened even after I had removed and reinstalled texmf and tetex. When finally I removed the old updmap.cfg manually (it wouldn't go away with 'fink purge -r texmf'), which I had edited when adding new fonts to my system, and reinstalled, everything worked perfectly. My manually added fonts where exported to the relevant directories in the new .texmf tree.
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