I have been running ISPConfig 2.2.6 for years. I have added a new domain and checked both the "DNS" and "DNS MX" boxes to host DNS for this domain and include a MX record. I have added a MX record via ISPConfig. The ISPConfig interface shows the MX record correctly, but when I use any other tool to check MX records the MX record is not appearing. dig mx mydomain.com answers with the SOA record instead of the MX record. What could be wrong?
Then your ispconfig server is not authoritive for the domain. Make sure that you set your ispconfig server to be the primary nameserver at your domain registrar. Also be aware that it may take up to 48 hours until changes in dns get valid.