It seems the answer to this is extremely simple. Publish to a local folder on your machine and then use FTP to put the contents of this folder on the web server.
I have an excellent program called SyncBackSE which will watch a directory for changes and do the second step automatically. Thus I end up with a one-step deployment.
As a plus, I get a local copy of a deployment on a given day which is dead easy to back-up, for belt-'n'-braces safety.
This idea was given to me in the following post and this does work despite the unrelated problems I was having in my original question above: c# - How to publish ASP.NET MVC site with File Zilla using FTP - Stack Overflow
Hope this helps someone.