It has nothing to do with the saved game, it's a built in renpy feature (skipping). So you have to set it up properly once you install a new version. Go to the main menu (Press escape if in game) then / preferences / skipHello,
As another user reported it, for me pressing Ctrl doesn't skip scenes anymore (whether I have seen them before or not). It worked on 0.8.3, but since I upgraded to 0.9.1 pressing Ctrl doesn't do anything anymore. I just copied my saved game from version 0.8.3 to the directory containing version 0.9.1 to play it, maybe that's what led to the problem?