I installed a new printer driver for a separate issue and my checks started printing starting in the middle instead of on the left. 

I had to go to File / Printer Setup / Checks / Options / Advanced and change my paper size to A4.  Immediately my checks once again started printing on the left rather than in the middle. One hour of my life used up, but I'm back to printing checks!

I had to use the following path:

File

Printer Setup

Check Paycheck

Options

Advanced

Change Paper size to A4

Boom! My checks went back to printing starting on the left instead of in the middle.

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. 

Short answer...I fixed it, thanks to bits and pieces of what I read from participants on this thread...the advice from QB seemed same old same old....read the script.  My problem was with my printer set up (scale)...was set to 82%...set that back to 100% and continued with the QB alignment tool...now I noticed the incremental changes were greater...(and also struck me in retrospect, the problem checks font was smaller than usual).  Ultimately I returned the horizontal and vertical adjustments back to "0" and WALLAH!  PRESTO!  

I only wish the suggestion to check printer setup scale is offered up front by QB.  BTW...I was very happy with my QB Desktop Pro 2019 (stand alone) program until, it stopped uploading QB) files, which I'm convinced was QB sabotage via updates.