Yes - I thought that issue had been resolved, but apparently not. Any accessing of the Editor GUI (i.e. to try to enable Advanced File Management) creates a fresh HTML Editor in the root directory, and updates the open pages to look for the connections folder in the root also- not that that's a big problem. So I'm assuming that this installation (unless one doesn't need to edit anything at all) is built to have all files and folders in the root directory, which I can't have.
The only way round it that I could find was to create a duplicate site definition in Dreamweaver, and specify the CMS directory as the Local Root Folder, thus forcing the HTML Editor to respect my preferred site structure. This works nicely, but shouldn't (in my opinion) be necessary. I thought the paths issues were sorted.
Would love to hear from someone who has managed to get the Advanced File Management features working. The ability to delete files that one has uploaded (without an FTP program) is, to my mind, a basic feature. Some documentation to explain the procedures would be nice too.