Rapidweaver uses Mac OS preferences to populate its “Recent Items” menu. Unfortunately, there seems to be a bug with OSX Capitan that prevents the listing of recent files. Strangely, this doesn’t happen with all OSX programs.
I’ve tried downloading the TinkerTool program but there was no change.
Have you noticed any special circumstances where recent items stop showing up? It never happens on my Mac – no matter what application (I use El Capitan, too), unless I reset the Recent Items…