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Jon: My build had and continues to have the same issue you described. Has your problem remained remedied with twisting and shortening the S1 wire? I have tried that and mine continues to shake, and jump around a few seconds after starting.
Does it help performance if the device is near balance without anyone on it?
Below is my device and it is not well balanced. Developed a problem while starting up: After running for 30 seconds to a minute, it goes crazy and stays crazy until I reset the Arduino. Could my messy wiring that looks like a bird next be the source of the problem.
Below is a pic of my poorly balanced Segway. Problem has surfaced as I test the unit before tidying up the wiring. It seems to run okay for 30 sec to a minute, then it goes haywire. Motors stop and start violently and Arduino must be reset. Could my messy wiring be the source of this problem?