Once a self signed certificate is added to the Security - SSL Integrations section in configurator you can not over write it again later using Configurator.
The logging you do get doesn't show a problem and it looks like the orch should have run but the event never makes it to the AlfEventManager log. We should either log this connection failure somewhere or at the least make the Test Connect button fail in the Repository when there is an SSL Connection issue. This Test Connect button should also pertain to Endpoints in the Endpoint area in Repository as well as the Target Servers area.
Connecting using Composer to an Application Repository using IPv6 throws an SSL certificate error. Composer cannot be connected - SSL certificate is invalid according to validation procedure.