Yeah, story progression was a function that got implimented in the final few hours, so it's propabbly the buggiest part.
If it helps, to get your story back to the point where stars count, enter into your console "gdata.story = 12", and that'll bring the automation back, and unlock any further sections your stars unlocked.
oh, thanks, i;ll keep in mind in case i case the situation again, but i managed to get to second mana absorb (with 440 star power thanks to some smart star respecs along the way and a lot of manual clicking) and after it the story caught up and it;s back to full auto. which is really good because without it and without you sharing the command i was considering quitting it rather than to start over... im glad i dont have to do either :)
