Shell – Why have wireless controls disappeared from the GNOME topbar

Well your first link is about kernel mode arbitraty code execution there is not much you can do against that. Logging out won't help. Grsecurity and PaX could prevent this but I'm not sure. It surely protect against introducing new executable code but I can't find any evidence that it randomizes where the kernel code is located which means an exploit could use the code already in executable memory to perform arbitrary operations (a method known as return-oriented-programming). Since this overflow happens on the heap compiling the kernel with -fstack-protector-all won't help. Keeping the kernel up to date and people with pendrives away seems to be your best bet.

The second method is the result of a badly written screensaver which means logging out prevents that particular bug. Even if the attacker kills GDM he will not get in. Try killing it yourself from SSH. You get a black screen or a text-mode console. Besides AFAIK GDM runs as root (like login) so the attacker would need root privileges to kill it.

Switching users don't have this effect. When you switch user the screen is locked with the screensaver and GDM is started on the next virtual terminal. You can press [ctrl]+[alt]+[f7] to get back to the buggy screensaver.

When you edit the wireless settings you need to make sure that "Available to all users" and "Connect automatically" checkboxes are enabled and it will be available to everyone automatically. Early versions of Network Manager for some systems did not have "Available to all users" enabled by default (yours might be one of those systems) and the symptoms you describe are exactly the behavior that is supposed to happen with configuration setting. That was a confusing default setting for most people, so now the default is to have it enabled (at least it is for Ubuntu).

You can also check from the command line what devices and connections are managed by NetworkManager:

$ nmcli dev
DEVICE     TYPE              STATE        
wlan1      802-11-wireless   connected    
eth1       802-3-ethernet    connected    
$ nmcli con
NAME                      UUID                                   TYPE              TIMESTAMP-REAL                    
Yak n Yeti                b4e05828-e57e-4399-96aa-6cd988ee4975   802-11-wireless   Thu 27 Dec 2012 07:30:19 AM PST   

The settings are stored in /etc/NetworkManager/system-connections/ and you'll want to make sure that autoconnect=true and that either the users you want are listed permissions=user:whoever:root:; or the equivalent of "Available to all users" which is permissions=[];

[connection]
id=Yak n Yeti
uuid=b4e05828-e57e-4399-96aa-6cd988ee4975
type=802-11-wireless
permissions=user:whoever:;
autoconnect=false
timestamp=1355439451

[802-11-wireless]
ssid=Yak n Yeti
mode=infrastructure
mac-address=24:77:05:FF:97:BC
security=802-11-wireless-security

[802-11-wireless-security]
key-mgmt=wpa-psk
wep-key-flags=1
psk-flags=1
leap-password-flags=1

[ipv4]
method=auto

[ipv6]
method=auto