After finishing Chapter 2 I got immateriality into Chapter 4 (shown when you hit Esc). Also all map is opened. So, when I got “The Ruined World” quest which is in the beginning of Chapter 3 it was shown as Chapter 4.
It seems to be ok other than map and Chapter #, quests and portals are as it should be.
Probably because I played in 0.9 and something went wrong with old data.