Issue
Adafruit_BBIO PWM does not work Linux 4.9 kernel.
I will update with more information about the issue and my progress as I work towards resolution. I wanted to quickly log an issue so that the problem is visible to everyone.
Workaround
Use the Linux 4.4 kernel
cd /opt/scripts/tools/
sudo git pull
sudo ./update_kernel.sh --lts-4_4
sudo reboot