I've migrated portage and overlays metadata cache to sqlite (since sometimes eix takes too many time to update all the cache on some servers) and noticed that overlay markers ("[number]") is disappeared from eix output (see eix.log attach). Reproducible: Always tried on =sys-apps/portage-2.2.0_apha194 and _apha196
Created attachment 355688 [details] eix.log
eix-update is fixed in git master on BerliOS (>=eix-0.29.4). You can use the eix live ebuild from the mv overlay to test. As an unrelated note, if you use sqlite mainly to speed up eix (instead of portage), it might be faster if you generate metadata, see the SPEEDUP section in the eix manpage.
+*eix-0.29.4 (10 Sep 2013) + + 10 Sep 2013; Ian Stakenvicius <axs@gentoo.org> +eix-0.29.4.ebuild: + version bump, fixes bugs 480604, 483392 +