What did the camera sound like running? Was it loud at all?
If your pitch isn't adjusted, it can give you an unstable image like this, but it would make one heck of a racket. The SL is a pretty quiet camera, but you'd be able to hear it.
I'm still not sold on it being a scanner issue.
Pitch adjust will reduce the noise, but has no bearing on the stability of the image. The reg pins makes more noise if the film is being advanced to a spot not exactly aligned with the pin, but once engaged the film is registered correctly and will not move, and exposure occurs after the pins engage.
The usual practice for a shoot of any importance is to shoot a steady test to eliminate any questions about camera stability, but in my experience Moviecams are pretty reliable.