digitalslavery: of course it is a web site project.
:-)
I had a suspicision (in future, that is extremely relevant information to incldue, different project types to behave very differently with respect to defining project content and actions on that content).
Just doing a test here, any everything works as expected (need to refresh and items appear), so there is something local.
Can you re-create this behaviour locally (e.g. create new web site and then create items under it locally in explorer then refresh): i.e. is it just this one project or any? Do other developers see the same behaviour with this project?
What form of source control are you using?
Richard