It seems that there is a limit for the height of the Diagram, which is set to "20000px". After that height, every pixel over that height will be appended as an empty space before the shapes. Currently, what I could suggest is to enable fix the height to "20000" at most and move down to the next shapes with "CTRL+drag".
I will contact our developers to see if there is a particular reason for that hard-coded value and if there is none, we could change it to a higher value. If I find a quick workaround for changing the value, I will get back to you with an example.