Bug solved, fix is very simple.
How to create bug:
https://dom.com:10000/config.cgi?virtual-serverExtra Webmin modules for server administrators: select password protected dirs
Then enable under 'Extra modules available to server administrators ' (mind the small difference) the
'password protected dirs', set it to yes.
Find all the existing protected dirs by /.
Then remove the first protected dir option again and let the lowest protected dir on yes.
Users will still have full access to all protected dirs!
Other BIG BUG:
When you set 'Scheduled Cron Jobs (user's Cron jobs)' to yes, a user can simply input the following command in the cron:
ls /
He can then see everything hosted!