A few random thoughts..
Do you have the chain of actions added to each clickable element? If so, the use of actiongroups might make it easier to fix. Add groups for each needed chain of actions… on the clickable elements just add a runGroup action.
Timers are unreliable at least. I try to stay away from them whenever possible. Maybe thats possible when using actiongroups. Add a check at the end of each actiongroup whether the variable is set/ the user wants to skip the game.
PS. a sample of your Lectora might be helpfull