Tested this in VirtualBox:

Custom Xubuntu 12.10 installation (netinst with Xfce packages) - fully updated: 
not fixed
Stock Ubuntu 12.10 installation (installed with ubiquity, unmodified) - fully 
updated: not fixed
Stock Xubuntu 12.10 installation (installed with ubiquity, unmodified) - fully 
updated: not fixed
Fresh custom Xubuntu 12.10 installation (latest netinst with Xfce packages) - 
fully updated (while installing): not fixed

Tested this on my testing machine:

Custom Xubuntu 12.10 installation (netinst with Xfce packages) - fully updated: 
not fixed
Stock Xubuntu 12.10 installation (installed with ubiquity, unmodified) - fully 
updated: not fixed
Fresh custom Xubuntu 12.10 installation (latest netinst with Xfce packages) - 
fully updated (while installing): not fixed


In each and every case, purging dnsmasq-base solves all issues. Purging only 
network-manager only solves the long shutdown time, but not the unmounting 
issue.


Am I really the only one noticing the huge increase in shutdown time compared 
to 12.04, and hasn't anyone else seen fsck show up in every dmesg log?

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https://bugs.launchpad.net/bugs/1058987

Title:
  In Quantal, the root filesystem is not cleanly unmounted at shutdown
  or reboot

Status in “network-manager” package in Ubuntu:
  Incomplete

Bug description:
  Ever since some update in the Quantal pre-releases, having dnsmasq-
  base installed will cause the root filesystem to not be properly
  unmounted on shutdown and reboot. In case the Plymouth splash screen
  is disabled, the message 'mount: / is busy' will be shown, but
  otherwise the user will not even be aware of this problem.

  After rebooting, the root filesystem needs recovery, as shown in
  dmesg:

  kevin@vbox-xubuntu-quantal:~$ dmesg | grep EXT4
  [    1.022746] EXT4-fs (sda2): INFO: recovery required on readonly filesystem
  [    1.022750] EXT4-fs (sda2): write access will be enabled during recovery
  [    1.248294] EXT4-fs (sda2): recovery complete
  [    1.248661] EXT4-fs (sda2): mounted filesystem with ordered data mode. 
Opts: (null)
  [    1.456315] EXT4-fs (sda2): re-mounted. Opts: errors=remount-ro

  Yet again, the user will not be aware of this until it is too late.
  The only way to avoid this from happening (or at least what I've
  found) is running 'sudo apt-get purge dnsmasq-base'. Sadly, this also
  removes network-manager and network-manager-gnome, so it isn't really
  a viable solution.

  Another problem that might be related is that having an active
  connection with the Network Manager prior to shutting down or
  rebooting, will cause the process to hang for a few seconds, after
  which the message about / being busy is shown. Stopping the network
  service (sudo service networking stop) will solve the hanging, but not
  the unclean unmount. So far, only purging dnsmasq-base seems to do
  that, which obviously also solves the other problem, as Network
  Manager will then also be removed.

  Although I haven't experienced it yet, this could cause potential data
  loss; especially for users without a seperate /home partition.

  
  ProblemType: Bug
  ApportVersion: 2.5.3-0ubuntu1
  Architecture: amd64
  Date: Sun Sep 30 12:49:24 2012
  DistroRelease: Ubuntu 12.10
  Package: dnsmasq-base 2.63-1ubuntu1
  PackageArchitecture: amd64
  ProcVersionSignature: Ubuntu 3.5.0-16.25-generic 3.5.4
  SourcePackage: dnsmasq
  Tags:  quantal
  Uname: Linux 3.5.0-16-generic x86_64
  UpgradeStatus: No upgrade log present (probably fresh install)

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