You apparently run Magellan on its own screen/window and/or didn't start it up with D2A/Magellambient.
As Magellan can't show PNG icons and other Ambient things, the purpose of D2A/Magellambient is to hide the original Magellan window and bring the functionality of it over Ambient. When you have those kind of problems, the original Magellan window hasn't been hidden.
Lets take D2A as an example as I'm using it nowadays. First set Magellan to use Workbench screen to avoid useless screen opening (Settings->Environment->Display->Workbench:Use). Then you have to disable backdrop mode from Magellan (from pulldown menus Opus->Backdrop) and I'd recommend you to resize Magellan window as small as you can get it to avoid too much visibility in startup, and then save layout (Settings->Save layout). Now you can test to execute D2A to hide the window and doubleclick Ambient desktop if you can get Magellan lister up. If you want to start Magellan automatically when you run D2A, add to D2A's tooltypes: "DOPUS_COMMAND=Run DOpus5:DirectoryOpus DETACH QUIET". Then you can have it copied in WBStartup to be run on every boot.
As Ambient also has option to open its window with doubleclick on desktop, you can configure D2A open Magellan lister with middle mousebutton too. Then you can open easily either Ambient or Magellan lister. Enable D2A's tooltype "MIDDLE" for that.
You can have Magellan's buttonbanks, startmenus etc over Ambient even when Magellan's main window is hidden. And you can get into Magellan's menus whenever there's its lister activated. Global hotkeys, scripts and most of the stuff will work even when no Magellan windows are activated, but some features like Icon Positioning can't be brought though..
EDIT: hmh.. is there option to disable smileys or something? That one line containing : and D was messed up...