When you tighten the screws, it can tweak the tube to one side or another.
I got myself a Burris MTAC w/ the QD PEPR mount, and was having the same issues.
What I was told to do by fellow members was to use a plumb line, and levels.
What I did was buy 2 cheap line levels and pop out 2 bubble levels.
I then used silicon double sided tape, and put one on my rail, and one on the top turret of my scope.
I found myself a nice level table, and put my upper on that. I could verify the upper was level and square with the first bubble level.
Then I mounted my scope. I also used a 6mm chord with a weight thumb tacked to my kitchen ceiling as a plumb line.
Once the scope was mounted I could use the 2 bubble levels to verify that the scope was level to my upper.
Then, I could also use the plumb line to verify that the reticle was square.
One thing to consider, I had the PA multi reticle M3, and the reticle itself was slightly off.
So I had to use a plumb line only with a leveled upper to get it square