A few things that might point you toward one system or another or toward wiring or other issue -
Does it happen all the time or it just starts up for some reason ? Once it starts how long does it do it or does it ever stop ? When it happens is the pulse occurring regularly as in every X seconds or seemingly random, etc.? Is the pulse a dimming or brightening of the lights? Does the frequency or intensity of the pulsing have either an inverse or direct relation to the engine RPM or any other action (e.g., does turning on the headlights or other system change the pulsing frequency or intensity)? Does the measured voltage level anywhere in the system pulse with the visible pulse?
Sorry to be playing 20 questions....just seeing if there is any lead to follow . Sometimes it's the one stupid question somebody asks that beaks the case....sometimes.