The customer has the package service installed on his SMP. It seemed to be running correctly but it was not publishing https codebases. The respective HTTPS codebases settings have been enable as per:
HOWTO93164 "Configuring a package server to publish HTTPS package codebase"
TECH171971 "Notification Server will not build https package download location links in IIS 7"
ITMS 8.0, 8.1
When running SMP and Site Server on the same host you can/t override the certificate used on the Site Server. The issue is that you'd have two web servers binding to port 443 using two different certificates. This is why it failed.
To correct the issue, turn off the custom communication settings for the Site Server hosted on the same server as the Notification Server. By doing so the Site server can leverage the same certificate used to communicate to the Notification server over HTTPS.
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