Regarding custom code, I was saying that you might be able to use custom code to override that absolute position. (Not really the best way to solve it tho)
At first I thought the image was aligning to your grid element. Still looks that way but I moved the light-box element outside of the grid altogether and the same issue occurred. I then tried dragging a brand new lightbox into the grid and got the same issue.
Have you tried removing the custom code from the page Head tag and test? Or maybe code in you site-wide settings panel?