Here is my view of the problem: On an up-to-date Maverick install, if
/etc/hosts looks like the following on bootup...

--------
127.0.0.1       localhost
127.0.1.1       hostname.intra.example.com      hostname

# The following lines are desirable for IPv6 capable hosts
::1     localhost ip6-localhost ip6-loopback
fe00::0 ip6-localnet
ff00::0 ip6-mcastprefix
ff02::1 ip6-allnodes
ff02::2 ip6-allrouters
--------

...NetworkManager changes it (syslog: "<info> Updating /etc/hosts with
new system hostname") to this:

--------
127.0.0.1       hostname        localhost.localdomain   localhost
::1     hostname        localhost6.localdomain6 localhost6
127.0.1.1       hostname.intra.example.com      hostname

# The following lines are desirable for IPv6 capable hosts
::1     localhost ip6-localhost ip6-loopback
fe00::0 ip6-localnet
ff00::0 ip6-mcastprefix
ff02::1 ip6-allnodes
ff02::2 ip6-allrouters
--------

With that, "hostname -f" incorrectly returns just the unqualified
hostname.

I think part of the problem is the layout convention being used for
/etc/hosts. The first example above was the result of the Ubuntu
alternate installer. On a different system installed with Ubiquity,
however, I have this (note that this system does not have a domain part,
so I can't tell if "hostname -f" is broken or not):

--------
192.168.1.XX    hostname        # Added by NetworkManager
127.0.0.1       localhost.localdomain   localhost
::1     hostname        localhost6.localdomain6 localhost6
127.0.1.1       hostname

# The following lines are desirable for IPv6 capable hosts
::1     localhost ip6-localhost ip6-loopback
fe00::0 ip6-localnet
ff00::0 ip6-mcastprefix
ff02::1 ip6-allnodes
ff02::2 ip6-allrouters
ff02::3 ip6-allhosts
--------

I think N-M's logic for modifying /etc/hosts may not be robust enough to
generate a correct file given some of these inputs.

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https://bugs.launchpad.net/bugs/8980

Title:
  hostname -f does not return a proper FQDN

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