Alternative start (The Elder Scrolls 5: Skyrim)

I use alternative start for SE and started a new game. Chose the path of play and thought. Sky and so is not a very stable game and became suspicious, and won't break the whole game, even stronger than in the version without AC. It is that the game is normal, and it happens that after starting a new game go awry, some tasks lag, the NPCs disappear....well who was not just Skye will understand what I mean)