This is such a broad question. Of course Branch aware means that lot more needs to be set up on runtime (quizzing system variables) and more navigation is needed as well. How many branches do you have, which devices and bandwidth was used by those users experiencing lagging, how did you limit navigation, how big is the course, was everything optimized? So many factors can be the cause. You may even use question pools?
You are about the first to mention this particular problem, I didn't see this appear yet, if my memory is correct.
Maybe this blog can clarify some aspects of Branch aware: