OMG, I just had a huge brainfart!! I had an issue on a Connections 5.5 CR3 site where the option to get notified about "Libraries" was in the GUI.

I had an issue with the IBM Connections Desktop Plugin. IBM introduced the "My Drive" and the ability to sync folders and sub-folders some months ago, and this seemed to be working fine when I connected the plugin to on-prem installations of Connections. I was able to sync folders, files and sub-folders.

I´ve done 5 different customer installations on IBM Docs 2.0 now, and they have all been having the same issues. When I´ve done the installations, I´ve also created a scheduled restart of the server once a week.