Delete your .emacs.desktop, and put in init.el:

(desktop-save-mode 1)
(add-hook 'deactivate-mark-hook (lambda () (setq cursor-type t)))
(add-hook 'activate-mark-hook (lambda () (setq cursor-type 'bar)))

Start Emacs 24.3, open a file, press C-SPC C-g, then exit Emacs and save the desktop, then restart Emacs. Notice that the cursor type is now a bar, not a block. It should be a block.

The attached patch fixes it. It could be fixed without patching set-mark, by conditionally calling deactivate-mark in desktop-create-buffer after calling set-mark, but that's a hack; the mark shouldn't be activated in the first place. Besides that, I need a dont-activate option for set-mark in some of my other code, so this bug gives me an excuse to add it.

The attached patch relies on the fix for bug 13027, which was reportedly applied last November, but didn't make it into 24.3, so either apply that to 24.3, or use the current development version, but I haven't tried the latter.