There were some big changes in the Pi3, the inbuilt Bluetooth adapter on Pi3 uses the serial lines and because of which you might not have the serial monitor working. You having enabled the serial communication through
raspi-config option, you will have to disable Bluetooth as well. To do this you can follow the tutorial here.
We have a custom image of stock Raspbian called the Raspbian for Robots which helps you to enable and disable serial lines with ease. You can install this image following the guide here and to enable the serial communication in our image, use the Advanced communication option from the desktop in the GUI and click Enable BrickPi/UART option.
Please let us know if this helps,