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Alright I put the Pi 2 in a cardboard box and held the flash at the same spot (but the box obscures the light). It keeps running just fine and doesn't have the nasty spike. Definitely is something light related.
Thanks! Well done. Photoelectric it is. Now I wonder what color its most susceptible to...
This property of diodes can be used in a fun way: LEDs emit light, but they can also be used as photodiodes[2]. It's easy with a microcontroller pin that can act as both a digital output and analog input. LEDs are of course not optimized for this use (small sensor area, the package may absorb useful light particularly in the UV, phosphor if present may get in the way), but they can be used as photodetectors. There's even an Arduino sketch[3].
1. http://image.slidesharecdn.com/lect12-photodiodedetectors-13...