I am running a basic servo test and have the Due powered via the 9V power as well as have it plugged in to the USB to upload the code. The servo is connected to the 5V and Gnd of the Due along with using pin 6 to control the servo. As long as I keep the Due plugged into the USB, the servo works fine. However, when I unplug the USB (where the power presumably is only supplied through the 9V input), the servo jitters. Why would this be?
The servo current draw is probably low enough to not exceed the USB limit but too much for the Due on-board regulator. You'll need a separate regulator for the 5V servo.