This is probably long fixed for you by now but I was bothered by the same issue for a week until yesterday.
The virtualmin interface was reporting wrong quotas etc, adding new users caused the same error you had I was quite frustrated and figured it was because I was using the free version that it did not work correctly
Then for the hell of it i figured I would turn off quotas and turn them back on. Boom, reporting is fixed, adding users fixed.
/var seems to only have usrquota. That’s actually where you need grpquota, since databases live there, and only grpquota can possibly apply. Unless you also have mail on /var (in mbox spools, which is not recommended) you would have little use for usrquota (though I think Virtualmin still wants it enabled).
I don’t know if that’ll resolve things…but, it’s definitely worth a shot (and if it doesn’t, filing a bug would be the way forward). Also, Virtualmin can’t really enforce quotas accurately if you have two partitions for user data (/home and /var), since quotas apply to each file system separately. So, if you set a 10GB limit, your users could have 10GB of website data and mail in /home and then 10GB of database data in /var, for a total of 20GB. This probably isn’t a huge concern. Just something to be aware of.
I experienced the same problem :
In Virtualmin fresh install create new server give me :
setquota: Not all specified mountpoints are using quota.
The file system of my server is fsx.
On the Configuration For module Disk Quotas I noticed the quota commands are for ext filsesystem
but as the quotas seems to work well I did not change it.
I then check
Webmin / System / Disk and Network Filesystem
there I check
/home and /var and noticed that /var only has Enable user quotas checked
but not Enable group quotas . So I allow group quotas and this solve it for me.
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Ced