I have created a custom overlay with ebuilds that fall into a custom category. If I don't put the category in a categories file in the overlay's profiles directory, eix does not see the packages/ebuilds, so I create the categories file. Ok, no problem. I can now emerge packages perfectly and see them with eix. However, I cannot do emerge --config for those packages. The ebuild used for emerge --config is the one that is saved in the /var/db/pkg/ tree but unfortunately and a bit to my surprise, there is no /var/db/pkg/<mycategory>, so no information about the installation is saved (without error message), in particular the ebuild itself is lost, and the emerge --config fails. Reproducible: Always Workaround 1: don't use custom categories. Workaround 2: add the category to the official categories file, but lose that info at official sync. I don't really like any of those, I would like use of overlays to be as flexible as possible.
Workaround 3: add your category to /etc/portage/categories, but I hoped that info could be delivered to the user together with the profile.
What version of sys-apps/portage are you using? Please post emerge --info output.
Latest stable, being portage-2.1.4.5.