My only suggestion is that it's to do with web virtual directories at the server
? Since .NET maintenace for server  staff is minimum, no registrations, no
setting errors pages, etc, no asking them to create  virtual directories.

VS.NET creates the virt dir when you upload it, it can be a bit confusing and if
you try renaming one they all sorts can go wrong that you can't do anything
about; indeed, from what I remember deleting a vd and then recreating the folder
as a non vd it will likely become a vd, don't know whether a server restart
sorts it, it's a pain.

I suggest you write to your host and ask them to check they are set up
correctly, makbe one of these sub folders has somehow become a virtual dir ?