Hi Tim,
Yes, after a calmer period and a lengthy discussion with a work colleague I've realised that it's not adding a 'folder view' as it was in 1.8, but actually adding a physical folder to the task area, which you then populate later with content.
I think my misconception seems to be that you could still upload files and create folders prior to setting up the links and structure on the actual course page. But this is not the case anymore, it seems that you have to load the files or create the folders as you're creating the course content.
I can see the bonus side of this, which helps prevent people simply dumping files in to a folder and leaving them there unused taking up space on the server etc ... But it's still a bit of a jump from one way of working to another.
I think the right path was taken in development, but there is very little in the way of signposts to guide you on your way down this new path. I hope that at some stage the process will be a little bit more intuitive.