If you really click on
https://zimbra.url.com:443/home/user....com/.?fmt=tgz It does not show extra '.' .
As per the error it seems to me :-
ERROR: service.FAILURE (system failure: GET from
https://zimbra.url.com:443/home/user....com/.?fmt=tgz. failed, status=501. not implemented yet)
https has the issue. Does the server have https enabled ? You tried accessing with http as per your manual test but if you see it gets redirected to https . Seems you have both/redirect enabled. You might want to research on this.