Some plugins require root-rights. So before installing from an updateSite do this:
sudo chmod 777 -R /opt/ibm/lotus/notes/framework/shared/eclipse/
sudo chmod 777 -R /opt/ibm/lotus/notes/framework/rcp/deploy/
and after installation
sudo chmod 755 -R /opt/ibm/lotus/notes/framework/shared/eclipse/
sudo chmod 755 -R /opt/ibm/lotus/notes/framework/rcp/deploy/
Now you can install the Lotus Connections plugins without any errors!