The default code is set to Arcade drive. This means that the robot is controlled by one joystick. The y-axis controls velocity, the x controls rotation.
I don't have the autonomous code in front of me, but from what I remember with playing around with it was that your description is correct. The default autonomous code is on a timer, and goes forward then turns (left I believe) for a short amount of time four times.
To me, it sounds like the default code is running perfectly fine. To switch to tank drive (two joysticks, each controlling one side of the robot), you will have to replace the Arcade drive VI with the tank drive VI, and add another joystick. You can also easily change the autonomous code (<A href="http://www.lvmastery.com/tipjar2009-01-02">LV mastery tutorial on autonomous</a>).
If you already modified you code, and it isnt changing anything, make sure your build specifications are correct, and that you are deploying the build to run as startup. If it isnt being run as the startup project, the old code will continue to be run every time you turn the robot on.