We have got this working now. There was a mis-configuration where the Active Directory SCP entry was left pointing to a previous Office 365 test domain so the computer was still Azure AD joined to this old Office 365 tenancy but Azure AD Connect had replicated it to the new Office 365 tenancy I was using and the computer showed up in there as well.


On the computer it is a good idea to use dsregcmd /status and check the tenancy ID that it is joined to if you are having issues and have been used different tenancies.