Steps to reproduce:

* Start session
* Try to connect to a network which needs a password; e.g. a Wi-Fi network.
* gnome-shell pops up the dialog to ask for the secrets; that's ok.
* Now restart NetworkManager (e.g. sudo service NetworkManager restart or whatever applies in your distro).
* Try to connect to a network which needs a password; e.g. a Wi-Fi network.
* gnome-shell doesn't pop up the dialog to ask for the secrets; wrong.

This issue seems to be introduced by the following commit:
------------------------------------------------------------
2a800e4ce0912f098b4a469fc7a680ad094b3bfa
Author: Jasper St. Pierre <jstpierre@mecheye.net>
Date:   Sun Sep 2 22:23:50 2012 -0300

    Rearchitect the Shell to have a components system
------------------------------------------------------------

One of the changes done in the commit is moving from:
  this._native = new Shell.NetworkAgent({
     auto_register: true,
     identifier: 'org.gnome.Shell.NetworkAgent' });

To:
  this._native = new Shell.NetworkAgent({
     auto_register: false,
     identifier: 'org.gnome.Shell.NetworkAgent' });

Some other changes were added in the commit; like new enable() and disable() methods in the NetworkAgent object, likely to register() and unregister() the network agent, but I didn't find any place where these were being executed.


If you relaunch NetworkManager with --log-level=DEBUG, you'll actually see that if using a gnome-shell snapshot before that commit we get the agent registered:
[nm-agent-manager.c:297] impl_agent_manager_register(): (:1.253/org.gnome.Shell.NetworkAgent/1000) requesting permissions
[nm-agent-manager.c:227] agent_register_permissions_done(): (:1.253/org.gnome.Shell.NetworkAgent/1000) agent registered

But no such log will be given if using gnome-shell git master or just git at commit 2a800e4ce0912f098b4a469fc7a680ad094b3bfa.

If you completely restart gnome-shell, though, it will register the agent correctly. Just on NM restart it won't re-register it, which it should.