You can check if /etc/NetworkManager/NetworkManager.conf just went missing using:
dpkg -S /etc/NetworkManager/NetworkManager.conf
My 12.04 has the following as content of /etc/NetworkManager/NetworkManager.conf:
[main]
plugins=ifupdown,keyfile
dns=dnsmasq
[ifupdown]
managed=false
You might be able just to add that content, and edit that if the file got accidentally deleted. In /etc/NetworkManager/dispatcher.d/ I have only the file 01ifupdown, make sure that it is there.
If it has gone missing you can re-install the entire NetworkManager package like so:
sudo apt-get --reinstall install NetworkManager