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.