After installing the Connections plugin for IBM Notes I couldn't seem to get either Files, Activities or Status Updates to work. I could however connect to Greenhouse with no issue. I also reach my Connections server via the web or via the desktop plugin as well.
Another oddity was that none of the other integrated Connections
components would work such as the business card integration in Sametime.
It turned out to be SSL related. Specifically, I use IBM HTTP Server to front end Connections and use a URL rewrite to force any incoming HTTP traffic to use HTTPS instead. It appears that the Connections plugin for Notes had an issue with that URL rewrite.
In order to force the plugin for Notes to use HTTPS only, I changed the LotusConnections-config.xml file to point all static href parameters to be https instead of http.
Then I reset the Connections back to defaults, entered the server, my user id and password and applied the changes. This changed all my Accounts to use HTTPS. Once I did that, all parts of the Notes plugin worked perfectly. Of course, if you have a similar issue you can test this yourself manually by changing the Accounts one at a time and see if it helps you.