/usr/share/texmf/pdftex/config/pdftex.cfg should be marked as a configuration
file. Most Type 1 font packages that require addition of map files to the dvips
configuration files will also require modification of pdftex.cfg.
This applies to tetex <= 1.0.7-64.
I fully agree. Just noted that my mathematica fonts were gone after the upgrade
to 9. This should definitely be marked as config file!
Should be fixed in 2.0.2-7.