Very similar issue was posted here, I do not believe they are the same.
We are running IBM Cognos Business Intelligence Server 10.2.2 (no other extra software products) on WebSphere Application Server BASE version 188.8.131.52, both softwares on an AIX server version 7. We are trying to configure RSA SSO through basic HTTP authentication from WebSphere to Cognos. For authentication, We are using a custom authentication provider for both WebSphere and Cognos.
We are using two WAS profiles, one for running the Cognos Servlet Gateway (for patterns matching /ServletGateway/*) and the other for running the Content Manager and Reporting Services (for patterns matching /p2pd/servlet/dispatch).
After editing and deploying the Cognos CJAP jar (custom java authentication provider) and doing the changes to .../war/gateway/web.xml and .../war/gateway/application.xml.template, building new application EARs and deploying them, login works just fine... I am challenged for username and password, entering the correct credentials will log the user into the cognos portal. When viewing the http header, as expected, Remote_User is null.
Things go wrong when we attempt to enable SSO. In WebSphere, we enable global security, setup the certs between the two profiles, etc.. and after doing so, Remote_User is not populating.