both /etc/init.d/checkroot and /etc/init.d/checkfs launches the normal fsck without parameters, which makes freebsd's fsck check all filesystems regardless of their "clean" status. To check the filesystems only if they are NOT marked as clean fsck must be run with -p (preen), as is described in fsck_ffs(8).
Thanks, I've overseen this in the new baselayout code. I fixed this in SVN but I'll wait before a new baselayout snapshot as I want to fix rc-daemon, too.