I've managed to fix it myself.
I removed the SRM license from the protected site Vcentre server completely, readded it and assigned it to the Vcentre server again. This brought back the correct count of VMs in the SRM system but still wouldn't allow me to add my additional VM until I rebooted the Vcentre server.
Now my only problem is that in my protection group the newly added VM's status says Replication Warning and I can find no other references nor errors for it. I hate this VMWare stuff. It tells you nothing helpful.