I believe the reason for this is that when you created the availability group in ssms you had to specify the cluster type.
The options were
There is another option but it would not of shown up and this is Windows Failover Cluster yet it is not listed.
Unless this option is selected you will not be able to manage The AG role via the cluster manager.
For some reason if your remove the Availability Group and recreate the Windows Failover Cluster is listed. I would recommend once you have remove the group please disable the Always On Availability Group feature in the Configuration manager and then re-enable to this seems to give it a kick.
To check if this is defiantly the reason select the properties of the Availability Group in SSMSand check the cluster type. If NONE or EXTERNAL are selected then this confirms it.