Upgrading to MySQL 4.1.14 with FEATURES="collision-protect" caused it to choke on two preexisting log files: /var/log/mysql/mysql.err /var/log/mysql/mysql.log which apparently were not claimed by the already-installed MySQL 4.0.25-r2 ebuild. Of course, the workaround is trivial, but it would be nice if it Just Worked(TM).
Improved to test the existance of a previous log directory. thanks
Reverted the bugfix, it was breaking stuff. More to come soon.
Fixed, some comment in Changelog