[EHaskins]

The WPILib "RobotDrive" class includes the ability to easily reverse motors in software. Normally this would be configured using a call to SetInvertedMotor().

WPILib code a docs:

/*
 * Invert a motor direction.
 * This is used when a motor should run in the opposite direction as the drive
 * code would normally run it. Motors that are direct drive would be inverted, the
 * Drive code assumes that the motors are geared with one reversal.
 * @param motor The motor index to invert.
 * @param isInverted True if the motor should be inverted when operated.
 */
void RobotDrive::SetInvertedMotor(MotorType motor, bool isInverted)
{
 ...
}

The OTB code probably was configured to reverse one side, since that is almost always desired for a robot drive.

EDIT:
After looking at the Default code and WPILib code, I found where it happens.

For the right side, reversed is considered forward. So, if you want the right side to rotate the same direction as the left you need to call SetInvertedMotor for the right drive motor(s) and set them to inverted. You can see this in the function RobotDrive::SetLeftRightMotorSpeeds.

Bold comments mine

/** Set the speed of the right and left motors.
 * This is used once an appropriate drive setup function is called such as
 * TwoWheelDrive(). The motors are set to "leftSpeed" and "rightSpeed"
 * and includes flipping the direction of one side for opposing motors.
 * @param leftSpeed The speed to send to the left side of the robot.
 * @param rightSpeed The speed to send to the right side of the robot.
 */
void RobotDrive::SetLeftRightMotorSpeeds(float leftSpeed, float rightSpeed)
{
	wpi_assert(m_rearLeftMotor != NULL && m_rearRightMotor != NULL);

	leftSpeed = Limit(leftSpeed);
	rightSpeed = Limit(rightSpeed);

	if (m_frontLeftMotor != NULL)
		m_frontLeftMotor->Set(Limit(leftSpeed) * m_invertedMotors[kFrontLeftMotor]);
	m_rearLeftMotor->Set(Limit(leftSpeed) * m_invertedMotors[kRearLeftMotor]);

	if (m_frontRightMotor != NULL)
//Notice the "-" before Limit(), but not on the lines above. This is where the right side is reversed.
		m_frontRightMotor->Set(-Limit(rightSpeed) * m_invertedMotors[kFrontRightMotor]); 
	m_rearRightMotor->Set(-Limit(rightSpeed) * m_invertedMotors[kRearRightMotor]);
}