Quotas are not working. How can I fix them ?

Check for quota support on the mounted filesystems:

FreeBSD:
Output of `mount` , look for "with quotas".
/dev/ad0s1h on /home (ufs, local, with quotas, soft-updates)
In /etc/fstab
/dev/ad0s1h /home ufs rw,userquota,groupquota 2 2

Linux:
Output of `mount` , look for "usrquota".
/dev/hda6 on /var type ext3 (rw,usrquota)
In /etc/fstab
LABEL=/var /var ext3 defaults,usrquota 1 2

If the entries are missing from /etc/fstab, add them. If they are present, verify that there is support for quotas in the kernel and that any relevant modules are loaded.

Check that the quota files are present and not zero byte files:
FreeBSD:
-rw-r----- 1 root operator 2097120 Apr 30 16:19 quota.user

Linux :
-rwxr--r-- 1 root root 8192 Dec 26 20:18 aquota.user*
-rwxr--r-- 1 root root 2097120 Apr 30 04:19 quota.user*

If these files do not exists, run /scripts/initquotas. If they do exist, but quotas are not working, you can either delete the quota files and run initquotas or run /scripts/fixquotas.

After this, repquota -a should print out the soft/hard limits with grace periods for all users.

If quotas are still not reporting anything in WHM and/or cPanel, check /var/cpanel/cpanel.config for
* disablequotacache=0

If that is set to 0, try setting it to 1 and see if that fixes it.