Autonomous Code Only Activating For 1 Second

After a stressful day of competition, our auton only drives for about 1 second before stopping, or maybe even less than a second. I’m using a chooser to determine which auton logic to use, and it should activate from there. Here is the code


	@Override
	public void autonomous() {
		ds = DriverStation.getInstance().getAlliance();
		String selectedPosition = position.getSelected();
		/*
		 * Initialize settings for used subsystems
		 */
		if (reset < 1) {
			drive.setMaxOutput(0.75);
			gyro.reset();
			reset++;
		}

		this.updateDashboard();

		/*
		 * Blue Alliance
		 */
		if (ds == DriverStation.Alliance.Blue) {
			this.auton(selectedPosition, 1, 1);
		} else if (ds == DriverStation.Alliance.Red) {
			this.auton(selectedPosition, -1, -1);
		} else {
			DriverStation.reportError("DriverStation is invalid", true);
		}

	}
	public void auton(String position, double side, double turn) {
		/*
		 * Note: positive = backwards & left negative = forwards & right
		 */

		/*
		 * Position 1
		 */
		if (position == RobotMap.POS_1) {
			drive.mecanumDrive_Cartesian(1, 0, angle, 0);
			Timer.delay(3);
			drive.stopMotor();
			this.lineUp();
		}
		/*
		 * Position 2
		 */
		else if (position == RobotMap.POS_2) {
			shooter.set(this.getShooterSpeed());
			drive.mecanumDrive_Cartesian(0.5, side, angle, 0);
			Timer.delay(3);
			drive.mecanumDrive_Cartesian(0, 0, turn, 0);
			Timer.delay(0.1);
			drive.stopMotor();
			Timer.delay(0.5);
			this.lineUp();
		}
		/*
		 * Position 3
		 */
		else {

		}
	}

Position refers to a SendableChooser with options “Position1”, "Position2, and “Position3”.

http://wpilib.screenstepslive.com/s/4485/m/13810/l/241863-using-the-motor-safety-feature