Deleting the files in that folder is not the correct way to uninstall, but if you did this, what is happening is that the installer is checking for the existence of a number of commander* files in /etc/init.d. If it finds them, it assumes that you are performing an upgrade, and not a clean install. Delete the files:
sudo rm -f /etc/init.d/commander*
...and run the installer again. It should work fine now.