Issue with syncing in scenario scenes

Without seeing the *story file, it's a bit challenging to deduce what could be going on. But you might try a couple of things to keep separate scenes. First, insert a neutral slide after the first scene that offers some meaningful feedback or provides a "clean slate" for the second scene. In some cases, I've just used a literal blank slide with a "Next" or "Continue" button. The purpose of the slide is only to keep the two scenario setups separated. 

A second recommendation is that you do not duplicate the first scene to make the second. This is especially problematic when you have logic actions (triggers, variables) in the first scene that you try to manipulate in the second to produce the desired outcome. I've found that building the scenarios from scratch (copying elements of the first scene, but not the entire slide) works effectively.