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I apologize for reviving this old thread, but it wasn't resolved and there is no much information about this (common) issue.
In my case, for some reason, the "other" category space was incorrectly calculated.
For some domains with only 500 to 900 MB of real space consumed, the stats showed about 2GB in the "other" category (dangerous as it can lock domains out of space).
I solved it executing the following command:
/usr/local/psa/admin/sbin/statistics --calculate-all
Or only for one domain:
/usr/local/psa/admin/sbin/statistics --calculate-one --domain-name=thedomaintocalculate.com
A very good script for calculate real space consumed by the domains is here: http://blog.aclarke.eu/a-simple-treesize-shell-script-for-linux/
It works as the treesize windows utility, if you execute it in the /var/www/vhosts/thedomaintocalculate.com you can see the real space consumed from this domain, and the results are sorted by size.
(NOTE: I have nothing to do with the author).