I have installed Calibre using Ubuntu Software Centre on Ubuntu Gnome 13.04. Then, I knew that there is newer version at Calibre's website, so I installed the newer version following the site's instruction. Everything is ok except that I have two Calibre icons. How to solve it?
Seems as if you downloaded both versions and now you have both on your PC. Instead of downloading new one, uninstall the old one first and then install the new one. Or upgrade the old one if possible. So for you, I would uninstall (both) and reinstall.