If you upgrade to 3355 from a previous installation, portage will install the latest version then proceed to uninstall the previous version. The problem is that it will uninstall ALL the data files, leaving you with a b0rked installation and forcing you to yet another painful installation from the CDs.
Steps to Reproduce:
1.upgrade to 3355 from a previous ebuild
2.let portage do the rest
UT2004 installation was rendered unusable
Should have applied the patch, removed any old files (if necessary) and be ready
to play immediately.
This is by design.
You need 3 packages to play ut2004 now:
games-fps/ut2004-bonuspack-ece (technically not *required* but it is installed anyway)