The problem seems to be when you hold down the mouse button to continue painting. It works as expected on single clicks.
1. 32 x 32 canvas
2. Zoom 3600%
3. Turn on pixel grid
4. Choose pencil tool
5. Click on a box; while the mouse button is still down, move to the next box on the right (it paints to the top of the first box)
The problem seems to be when you hold down the mouse button to continue painting. It works as expected on single clicks.
1. 32 x 32 canvas
2. Zoom 3600%
3. Turn on pixel grid
4. Choose pencil tool
5. Click on a box; while the mouse button is still down, move to the next box on the right (it paints to the top of the first box)