I ma not sure if I have mentioned it, however maybe something useful:
I cannot dig records from my server from other hosts - they are refused - so perhaps that is part of the problem?
I have checked the MyDNS.conf file and the only change that I have made to it is to enable recursive lookups to another one of my hosts.
I am concerned as my installation is now a week overdue as a result of this problem, and I have already spent at least 12 to 18 hours over the last week trying to figure it out. It is unfortunate because there are a lot of great features in the ISPConfig 3, however if it not going to work from DNS point of view, then I cannot use it and will have rollback my new server to ISPConfig 2 or another solution. This would in my opinion be unfortunate, so if you are able to help I would really appreciate it very much, thank you.