Out of curiosity, what happens if you use wpa_suplicant to configure WiFi rather than use the set up wizard? Might be worth a try if you have the stomach for a clean install.
I've set up wifi config through network manager, but I've also tried wpa_supplicant. I'm suspecting that whatever goes wrong happens early in bootup, but even reloading the kernel module after boot didn't seem to help. I'm pretty much ready to give up with the built-in wifi at this point.
Out of curiosity, what happens if you use wpa_suplicant to configure WiFi rather than use the set up wizard? Might be worth a try if you have the stomach for a clean install.