NetworkManager is the best way for end-users to configure their network I think these problems are happening with people who configured their networks using the command line using some cut-and-paste fiddling with pppoeconf or stuff in /etc.
To have NetworkManager manage all interfaces without editing ifupdown/interfaces files, this should work.
Check /etc/network/interfaces.
Press alt+F2 and paste in:
gksudo gedit /etc/network/interfaces
Remove everything but
auto lo
iface lo inet loopback
Then Check /etc/NetworkManager/nm-system-settings.conf
Press alt+F2 and paste in:
gksudo gedit /etc/NetworkManager/nm-system-settings.conf
set
[ifupdown]
managed=false
Restart computer or NetworkManager service.
From now on, only configure the network using the NetworkManager applet in the notification area (aka system tray).