mydomain.com indicates that the server, for which the certificate is for doesn't use it. It uses the default instead. You have to reconfigure Apache to use the new one by entering it's path and making sure it is readible by the server. The path to the key associated to the certificate is also important.
I can't tell You how to do that step by step because I don't have any servers with ISPConfig 3 at the moment. I can only show You a tip which can put You on the right way: http://www.faqforge.com/linux/contro...-controlpanel/
It's also important what is the certificate meant for: the control panel or customers. By default Apache has to have seperate certificates for every ip address/domain so it could give some trouble in case You'd like to have SSL virtual hosts. I'm not sure if ISPConfig 3 supports the new way of handling SSL for 1+ accounts with a single IP.