You probably have two versions of calibre installed, one from using those commands and one from your Linux distribution.

If you're using Ubuntu, Debian, or one of the many other distributions based upon them, enter the following command:

dpkg -l calibre

If anything comes up, you will have to uninstall it. In the aforementioned distributions:

sudo apt-get remove calibre

At this point, the new version should work. If it doesn't, rerun the command that you described in post #3.

If you are using another version of Linux, the commands that I suggested may be different.