I was also facing the same problem, while trying to install Ubuntu 12.04 Desktop automatically. It seems like the GUI is not taking the configurations set by kickstart.
But I was able to install Ubuntu 12.04 Server by this method. After installation, I have installed ubuntu-desktop packages so that I can make use of the GUI.
An alternative method is to download and install Ubuntu-12.04-alternate.iso. The installation is in text mode,so it accepts kickstart config file.
Regards,