I've crawled back a few versions to test this behavior and it seems to have been introduced in 3.3.2 or 3.3.3; I reverted to 3.3.1 and the issue is not present there.

Essentially whenever a pop-up window that has multiple pages appears, when you page down, any blank lines on the new page retain the lines from the previous page. This is specifically for any pop-ups that use the ASCII formatting as opposed to the graphical window which, as far as I am aware, does not use pages. When playing with any tileset or even the base ASCII version, this behavior can be observed. Easily demonstrated by running a tutorial in the deluxe edition, but pretty easy to find in the free version as well by viewing the "first time playing" dialog.