The fix to the problem is to change /etc/NetworkManager/nm-system-settings.conf from:
[main]
plugins=ifupdown,keyfile
[ifupdown]
managed=false
to:
[main]
plugins=ifupdown,keyfile
[ifupdown]
managed=true
Then run:
/etc/init.d/network-manager restart
and you're good to go.
In my case the problem started after installing the vlan package.