you can do as I written here
http://forums.contribs.org/index.php/topic,40737.msg205966.html#msg205966to regain control of your quota
I had this before
and it seems that is strike from time to time
I wasn't able to figure from where it is
first time was due the fact I forgotten to delete the affa backup
but after that I have observed into other fresh install
it seems that it exist some bug in CentOS Quota allocation is not SME related
if you look into bugzilla you'll find it for sure
in short you need to stop service which massively can change user quota ( if you have direct access is preferable to just unplug the network)
and put quota off, recalculate, than put it on
what is strange is that 2 days ago I had noticed this on 2 servers
and yesterday just solved manually (as always)
now you tell me that you have the same problem
this mean is "time related"