When opening xfce4-appfinder or xfrun4 from either a terminal, or using a keyboard shortcut, the window opens beneath other windows. Killing any running process first, or launching with the -replace option solves this problem.
Because it starts from a running instance, it needs a startup id (startup notification), so the window manager knows when the user launched the command (for focus stealing). So without startup is and focus stealing enabled, it will sometimes show below other windows. You can enable startup notification in the keyboard shortcuts for the command. From the terminal its not possible (well as a command line argument, but it requires a valid timestamp).