I changed the background color that is visible when hovering code (to black). For example when you hover over a method, you see its signature in a box; I mean the background col
Preferences -> Java -> Editor -> "Source hover background"?
Edit: OK, do you mean the tooltip type popup window? The background color of the View to show Javadoc can be set in Preferences "General -> Appearance -> Colrs and Fonts -> Javadoc view background" but if you mean a tooltip type popup then you might have to set this in your OS.