In my attempt to fix the same problem, I have come across the following that might be of help to someone that knows more...
1. If I select "none" under ISPConfig => Sites => Auto-Subdomain then I can access the webmail under www.mydomain.com/webmail
but it asks to either save or download the login.php under mydomain.com/webmail
2. Any other setting under Auto-Subdomain will result in not being able to use the webmail, UNLESS I try mydomain.com:8080/webmail or www.mydomain.com:8080/webmail
I guess an easy "fix" would be to go with Auto-Subdomain=none and redirect traffic from the non www to the www domain...