User a terminal and make the directory
mkdir -p ~/.config/indicators/messages/applications-blacklist/
Files in here should be paths to .desktop files which will be blacklsited on startup. The .desktop files in question are located in
so you can make symlinks from there to this directory. Thus
ln -s /usr/share/indicators/messages/applications/menuItem ~/.config/indicators/messages/applications-blacklist/menuItem
menuItem from the messaging menu. Run
to see what the names of the .desktop files are and look for the one mentioning Ubuntu One.
You can run
to see the changes immediately. Else, a logout should work as well.