I am still struggling to get this library working well on Stretch.
With a brand new load of latest Stretch IOT image ( 11-4-17) and no changes except your prerequisites and installation, I am getting a 900mS run time for setting a pin 100 times. The same code take 3mS running on Jessie. This problem is independent of Python version and I have tried both BBB and BBG.

Bill

`import Adafruit_BBIO.GPIO as GPIO
import timeit

pin = 'P9_14'

GPIO.setup(pin, GPIO.OUT)

def setoutput():
for x in range(1, 10):
GPIO.output(pin, True)
GPIO.output(pin, False)

run 5 times, 10 x 2 x 5 = 100 outputs

result = timeit.Timer(setoutput).timeit(5)
print('time to complete 100 sets = ', result)
GPIO.cleanup()`