I suspect what you are seeing is that notes below the staff can push the stickings down, and that's one at a time. To get them to align, you need to set a sufficiently large offset to clear the notes you are likely to have. But, the default style and certainly the MDL templates should do this by default.
If increasing the offset doesn't work for you, please attach your score so we can investigate further.
Comments
I suspect what you are seeing is that notes below the staff can push the stickings down, and that's one at a time. To get them to align, you need to set a sufficiently large offset to clear the notes you are likely to have. But, the default style and certainly the MDL templates should do this by default.
If increasing the offset doesn't work for you, please attach your score so we can investigate further.