Ive noticed that the if the RED EYE reduction feature is on the deer got very nervous and spooky because of the flickering flash. I have set my camera for 30 second and 2 minute intervals and the deer dont seem to mind the flash and go back to feeding. I think alot of the spooked deer problems could be from the sound of the shutter on less noise proof units and/or the redeye setting being on.
Ive gotten pics of the same deer 5 ft from the camera several days in a row so I dont believe it bothers them. At least with my camera setup.