You may also want to check quotas on boot. You can do this using a script to run the quotacheck command; there is an example script in the Quota Mini HOWTO. The quotacheck command also has the ability to repair damaged quota files; familiarize yourself with it by reading the quotacheck(8) man page.

Also remember what I mentioned previously regarding quotaon and quotaoff. You should incorporate quotaon into your boot script so that quotas are enabled. To enable quotas on all filesystems where quotas are supported, use the -a option:

# quotaon -a