I've had this debate with some hunting buddies for some time now. I am a big fan of infrared digital game cameras, because I love the ability to get scouting camera videos at night or dusk. I love video, because you can study your game and their movements much better.
My buddies have always had issues with the 'glow' from the infrared cameras. They believe that this tends to spook the deer, and state that a traditional game camera flash won't. Their arguments were that the game camera flash was like lightening to a deer. It flashes and is gone and won't spook them.
Well, you aren't going to get any nighttime videos with a flash camera, and I agree that while in video mode, I have had deer staring at my infrared sensors. I think that the infrared "flash" in picture mode, is much less likely to spook a deer though. Since it doesn't light up the area, I don't believe they are as apt to notice it, unless they happen to be staring directly at the sensors at the time it flashes.
Well, I stumbled across this video today showing a nice buck getting spooked by a game camera flash. Sorry guys, it looks like this refutes your argument.