I am in the same situation but with ball tilt sensor to wake up the Photon from deep sleep and record the time. It can detect the pin is HIGH while it wake up so I know it is wake up from a push button not due to time. I tested it with a push button first and it work well but it does not work every time with a ball tilt switch. Sometime it wakes up and could not detect HIGH. I think because the ball bounds in the tube so fast that before it during wake up the switch already off.
So, my question is, how can I differentiate from waking from ball tile switch or due to time. If i set up it wakes up every 10 minutes, but before 10 minutes it wake up by switch sometime. I could not find a way to differentiate how it wake up.