I found the offending line in SnapJS and fortunely it means that to fix this, I didn't have to edit SnapJS itself.
settings.element.style[cache.vendor+'Transition'] = 'all ' + settings.transitionSpeed + 's ' + settings.easing;
The fix was to set the transitionSpeed
setting to 0
. Now it still applies the transition but as it's set to 0 it's obviously not noticeable.