This is mostly caused by generating the incorrect CSR for the domain you want the SSL certificate for. You mentioned that you have a self-managed cloud server with us. You might have made a mistake when creating the CSR for your domain by only typing in the domainnaame.co.za not www.domainname.co.za. The CSR for www caters for wwwa and the non-www but the non-www does not cater for the www record. We received your CSR in a raw text and we are unable to tell if the CSR is for www or the non-www record. The order will be made on the CSR we receive and the SSL will be created according to the CSR being used. The results will be the once you are getting.
The are a two ways to resolve this type of issue depending on the SSL provider used to order the SSL certificate. Some providers allow a re-issue with a different CSR at no cost within a certain period of time. Some SSL providers will not allow you to re-issue the SSL certificate with a different CSR, they only allow you to order a new one and cancel the old one.