Some update-eix wrappers (paludis-hook-update-eix, for example) call update-eix with '-a $location' for all known repos. With eix versions prior to 0.13 this just worked and '-a /usr/portage' was disarced. However, now '-a /usr/portage' makes eix to index /usr/portage twice, once as main repository, and another as an overlay.
Thanks for the report. Should now be fixed in eix svn trunk (>=eix-0.13.2).
Closing sine eix-0.13.2 is now in the tree.