I have recently experienced this exact same problem. After discussing with the Lectora support team we determined that transitions were causing the problems. Specifically, if a navigation button is clicked during any other object transitioning all the navigation on the page locks up. The only solution we’ve found is to remove transitions.
I can understand why a button may not function during a transition, but why should that lock up all other navigation on the page even after the transition is finished.
Hope that helps!