Root filesystem / is not remounted readonly before the effective reboot or shutdown if quotas are active on it, causing an fsck at each system start. Normally, /etc/rc.d/init.d/halt contains a mount -n -o remount,ro / that seemed to work well in RH6.0, but it seems that now, quota must be stopped before trying to put / in ro. Messages are: mount: / is busy and then again the same message, caused by "remounting remaining FS readonly" in the halt script. So before mount -n -o remount,ro / I added a line: quotaoff -a It seems to work. Maybe an initscripts fix should be released, I know of people that had corrupted datas because of that.
Fixed in initscripts-4.58, will be in next Raw Hide release.