If cvs sync is setup in make.conf, emerge does the initial checkout with the following command: if not portage.spawn("cd "+cvsdir+"; cvs -z0 -d "+cvsroot+" co gentoo-x86",portage.settings,free=1): This also syncs empty directories and gives some false repoman errors if you run repoman over this fresh sync (ChangeLog/metadata missing). Adding -P to the checkout command would fix this.
supposed to be fixed in 2.0.50 which is stable now. If this bug is not fixed please reopen.