I have had the same problem, and quite by chance, I figured it out! You have to hit finish now, then go back and the changes you made to alignment will work. Not sure if it takes QBO a minute or two to catch up, or if you have to save the changes before they are implemented. Either way, after 100 sheets of paper, I logged out, then back in again, and it made all the difference. So I decided to see if I could avoid having to log out, and hitting finish now accomplished the same thing.