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I've seen a lot of stuff about this, but everything I've tried has not helped my problem.

I made a custom 1 px brush using the marquee tool (seems like the default 1px pencil should also work fine though) and I am finding it to be extremely inaccurate on my MacBook Pro (Retina, 15-inch, Mid 2014) running Sierra 10.12.6 (16G29)

I think I have the settings configured right with no options turned on in the brush palette and square pixel ratio turned on under view -> Pixel Aspect Ratio

The pixel grid seems aligned properly, yet when I go to make a mark using this custom 1px brush, or the 1px pencil tool, I get the following effect in many (but not all) cases:

enter image description here

The pixel will be drawn one or more squares away. What other settings could influence this?

I set up these squares for a sprite sheet using 20px by 20px squares, which seem to have formed properly judging by the grid.

2

I believe your problem is that you are snapping to the 20 px grid.

Turn off View/Snap To/Grid.

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