Has described in this upstream issue https://github.com/geneweb/geneweb/issues/420 , Geneweb-6.08 compiled with Ocaml-4.xx should not take sources from https://github.com/geneweb/geneweb/archive/v6.08.tar.gz. Geneweb crash randomly with this code. Instead ebuild 6.08 should use the 6.08 maintenance branches https://github.com/geneweb/geneweb/commits/distrib-6-08-ocaml-4-xx. Source code can be get with https://github.com/geneweb/geneweb/archive/distrib-6-08-ocaml-4-xx.tar.gz
app-misc/geneweb-6.08-r1 is now in the tree. It is patched with the distrib-6-08-ocaml-4-xx difference (http://dev.gentoo.org/~tupone/geneweb-6.08-ocaml-4.patch.gz)