Try replaying the last part of ep9, near the end, you will see some messages about "Exporting data" or something like that. When this happens, your save will be used in S2.
I did replay the whole S1 and got the same problem, then I just went some minutes back in the saves and it worked.
Hey, I tried going back and visiting the Hospital/Moghila/Ciara/Yoga in a different order, but game breaks after going to the four places.