Remote site discovery seems to fail

I have two webserver.
I configured aegir on them with password-less ssh login.

I can verify the remote platform ok.
I manually installed a website on the remote platform (the one where the AEgir database and front end is NOT)
I ordered for a verify of the remote platform.
The verify went ok and even did found theme that were inside the newly installed site directory
But the new site on the remote platform was not added to AEgir and brought into AEgir control.

I did not find that as a known bug.

Am I expecting something AEgir is not ready for yet ?
Or is there something obvious I should check or test, I scratched my head a bit but did not find something obvious ?

I was not able to migrate to alpha3 yet so if you think I should start there because work on server supports where done in it, I can do my homework and come back in a few days when I upgraded.
I just did not want to add another layer of change beforehand.

thanks a lot.