If you define your Webserver in WebSphere before you install your applications the apps/modules will not be automatically mapped to this server.
Same happens occasionally even if you have installed your apps before you Webserver.
I.e. if you want to map your Webserver manually to your IBM Connections installation you have to click hundreds of times inside the WebSphere Integrated Solutions Console or you use the following script which I created today:
If you already use Christoph Stöttners Connections Scripts from GitHub you are used to run the scripts through the cnxmenu.py. Right now this new script is not available in this menu but I will try to add it in future.
Have fun (and provide feedback if script works for you)!