To reproduce, hit "Create New World", change the world type to "Customized", hit "Customize", change a setting and then hit "Defaults". When it displays the resulting popup, moving your mouse still displays the hovered state textures and effects for the sliders and buttons in the background. See attached screenshots.

Edit: I just realized that only the menu buttons, but not the buttons inside the scrolling window, are deactivated when the popup is open.