The "quotacheck" command has to be done after a file system is mounted (and before the "quotaon" command is done). In rc.sysinit, the "quotacheck" command is done before the filesystems are mounted. I'll also submit my patch to repair this problem.
this should be fixed in the latest Raw Hide initscripts.
initscripts-4.48-1 (RH 6.1) still seems to do the check at the wrong place. I didn't test it, but it looks like it still won't work.