You are right, after the level with the 3 mages you will face the vanishing enemy for the first time. This enemy creates a smoke effect and that effect is causing the issue. I thought I had fixed this when I changed some settings but it turns out that it only happens the first time you run that level, afterwards it runs fine. 

Until I find a way to fix this, whoever is playing my game, once you reach that situation just press [ESC] and wait for the menu to appear. After a few seconds the game will unfreeze and you can resume playing! 

Very sorry for this :(