The new version contains an automatic key configuration process that launches the first time you enter the game after setup. This process has 2 steps, and the readme describes it in great detail. Once you are done, the mod saves your changes into a file and the config window should not appear again. (The readme also describes how to run the key config again if you need to.)
Is this what you mean?
No, the script didn't start automatically, I had to use startscript. Then I got the following, your messages were flickering while these others were on the screen:
http://img271.imagevenue.com/img.php?image=98723_ScreenShot16_122_590lo.jpg
http://img234.imagevenue.com/img.php?image=98728_ScreenShot17_122_260lo.jpg
http://img191.imagevenue.com/img.php?image=98732_ScreenShot18_122_207lo.jpg
http://img164.imagevenue.com/img.php?image=98736_ScreenShot19_122_520lo.jpg
http://img274.imagevenue.com/img.php?image=98714_ScreenShot20_122_425lo.jpg
These look like part of the chargen process. Maybe a conflict with another mod, though I don't have a mod that affects chargen afaik.
EDIT: I tried it with a another savegame, and the chargen messages didn't appear and the script started automatically. The step 1 and step 2 messages continued to flicker, but that was the only problem. I'll try some other things to narrow it down.