After the updating of tetex packages an extra directory has appeared in the system root: "/.texmf-var". (This directory contains only an empty subdir web2c and a file ls-R). At least both tetex-3.0-20.FC5 and tetex-3.0-29.fc5 are affected. It seems that update/install process expects the invoking under a user, and tries to write the ~/.texmf-var to the homedir of the user. The actual install knows nothing about "a user", or just has the empty HOME environment. And "private-user-config" subdir appears at the system root "/" ...
Weird, I cannot see it while installing tetex-3.0-29.fc5 to a pristine chroot. I'll try to install tetex-3.0-20.FC5 and to upgrade to tetex-3.0-29.fc5 to see what happens.
It seems that it happened at some previous updates of tetex. When I remove this dir before the updating to the latest tetex, it not appears after the update. IMHO if you cannot reproduce this issue, just let foo on it... :)
Ok, I tested the update from tetex-3.0-20.FC5 to tetex-3.0-29.fc5 and saw no /.texmf-var in root of the chroot -> closing NOTABUG, feel free to open another bug when some other breakage occurs though ;-)