During system boot, rc.sysinit calls /sbin/quotaon BEFORE the root partition has been remounted read-write. This causes quotas to never be enabled, until the partition gets fsck'ed one day -- at which point, it is mounted RW by the time quotaon gets called. Simply moving lines 69-72 below line 96 (initscripts-3.78-1) would resolve the issue, I think.
*** This bug has been marked as a duplicate of 703 ***