Pretty much says it all - I ran an emerge rsync, and then an emerge --update --upgradeonly --deep --pretend world and that message spits out. Seems the gentoolkit-0.1.19-r3 ebuild's hosed something up.
Ahhh... it's the --deep clause that messes it up. Looks like the /var/db/pkg directory needs all those ebuilds to get updated too?
gentoolkit already fixed rm -rf /var/cache/edb/dep* emerge sync emerge regen