I have encountered some anomalies with the Layout/Folder navigation with FM11... Fortunately the scriping to the Layouts worked fine. Certain layouts could not be navigated to from the menu... It would go to the wrong layout. I noticed this mainly with layouts that were not in folders, Particularly if they were on the lower part of the list. This may be a Menu bug... As I have seen this occur when selecting a file from the Window menu as well... It would select the wrong file the first time but be ok after.
Scripting is fine, yes. it mainly effects development. Users never have access to the list (and status-area) in my solutions anyway. But it still needs an extra step to target such a layout for the developer. And navigations is more confusing when not all of the layout-folder get listed. But thanks for sharing your experience.