Not sure about a light leak; you would probably see more of an edge burn or an orange tint. I think it might be something in the drive of the camera itself. I've had a very similar thing happen in Canon Scoopics and Bernie at Super 16, Inc. said that it was really hard to get everything to lineup correctly for a flawless film run on those cameras because when you adjust one thing everything else down the path changes and there's not that many adjustments you can make to a Scoopic. It wasn't made for features; more for football games and news b-roll.
An SR3 should be as close to perfect as you can get but if it hasn't been maintained well or just something got knocked out of alignment you could get that pulsing thing. Possibly something in the mag loading but I'd expect it was more in the film path somewhere in the camera itself.
For example, look at the sky in this video...
By the way, what stock did you use?