After a couple of weeks communication between ourselves and a Microsoft Support representative, we now know that there is a problem with the synchronisation between the Office 365 User portal and the SharePoint Online portal. We are assured that the problem is being fixed. In the meantime the only fix is to add users manually on the SharePoint Online portal. Currently during the testing stage this will not really be a problem. However this could be a huge issue in the future once the migration has taken place.