docbook2X installs documentation into /usr/share/doc/${PN} but it should go to /usr/share/doc/${PF}. At the moment there are two doc dirs (/usr/share/doc/docbook2X, /usr/share/doc/docbook2X-0.8.8-r2) as dodoc installs into /usr/share/doc/${PF}.
*** Bug 295313 has been marked as a duplicate of this bug. ***
Created attachment 235633 [details, diff] docbook2X-0.8.8-htmldir.patch doc/Makefile.am hard codes the value of htmldir. This patch removes that and if you then add to econf: --htmldir=/usr/share/doc/${PF}/html this then fixes it for me
+ 29 Jul 2013; Sergey Popov <pinkbyte@gentoo.org> +docbook2X-0.8.8-r3.ebuild, + +files/docbook2X-0.8.8-drop-htmldir.patch: + Revision bump: EAPI 5, port to autotools-utils eclass. Install html + documentation in proper location, wrt bug #296112. Thanks to Chris Mayo + <aklhfex AT gmail.com> for suggested patch