MPU6050 Pulsating output

I am using an MPU6050 in a quadrotor project, and for some reason all the outputs seems to pulsate every half second or so by a large amount that I have not been able to filter out to my satisfaction.

It only occurs while running the entire control routine and not when simply dumping measurements directly onto the serial monitor.

I'm using the I2Cdevlib library by jrowberg and an Arduino Mega2650.

Any idea why this could be happening or how to ameliorate it??