I also run 1920x1080. I installed Beta 13 by downloading it from here.
Scrivener’s pop-up boxes often appear in relation to where you clicked to cause them, and there should be some sort of spatial control on them, particularly if the app is full-screen. In the case that Scrivener is not full screen, the buttons might appear on screen, but they could just as easily appear off-screen, because their placement is not constrained to stay within the bounds of Scrivener’s own window. They shouldn’t necessarily be constrained after appearance to stay there (people might move them off-window for some reason), but their placement at appearance really should be constrained.