Version in portage is extremely old. Reproducible: Always
Created attachment 195050 [details] atheme-4.0.1.ebuild Has some hackery, but works well for me
Created attachment 195052 [details] atheme-4.0.1.initd updated init.d to reflect name change of the binary
See my new bug for atheme-5.0.1: bug 305411
i also suggest closing this.
*** This bug has been marked as a duplicate of bug 305411 ***