Need serious help!!

Ok...........The first problem I have is that my game wasnt saving my choices from episode 1. I did the whole pref.prop thing and it worked. Then after I stopped playing episode 3 at a auto save, I loaded the game later and it was back at episode 1!!!!!! So all the work I did from 1&2 is gone. So, I am redoing the game and I would like to know what I have to do to not run into these problems again???????????
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