I don't know. Its the great mystery of our time. People always says "never use sudo with graphical applications, use gksudo instead or you will break things". I have never experienced anything breaking and no one is able to provide an answer to why it should break.

Besides that, I see no point in using Automatix to install programs. Why install and use a program to run a program that installs programs, when a program to install programs is already there (apt-get)? You have to install it in the first place anyway, so why not just install the programs it installs the first time around instead?