Shapes not aligning with grid

Whenever I add a shape to a grid/page, it never aligns with the grid. It's always bumped down. It happens with any of the shape options. The screenshots show what I see with a rectangle. I can't find any setting to remedy this and any code I could think of doesn't work. Am I missing something?

@CooperWhite Hi! You might have some custom code affecting the alignment. Can you share your site URL for context? Include a section with only a shape so we can investigate the issue.

I did try the shapes on another site and they worked fine. So yes, there must be something in my custom code. Now to find it....!