So after a new domain is added will I have to change vmail permissions for newdomain.com folder and /var/www/clients/client*/web*/ - I assumed that ISPConfig sets permissions when creating domains, mailbox's, FTP-user's, sites etc. so that the client has the relevant permissions..?
ISPConfig sets all permissions, so there should be need to adjust them manually. There was a bug in ISPConfig 220.127.116.11 which has been fixed in 18.104.22.168, so if the site was created with 22.214.171.124 or you dont run 126.96.36.199 already, then it might be that some permissions were not corect. You should update your server to the latest available ISPconfig version.