The Doxygen in portage is a bit old. Reproducible: Always Steps to Reproduce: 1. 2. 3.
Created attachment 42276 [details] ebuild for doxygen-1.3.9.1 This is basically the copy of the 1.3.8 ebuild. Besides the KEYWORDS changes I removed the part from src_unpack() which manipulated the files doxygen_manual.tex and configure. I think this became unnecessary.
Adding to CVS now; tested with dot files (works nicely).