After investigating the issue, it seems like sorting is OK. On your screenshot 
the first five values ordered are: 
* 3:21:44 (3 hours 21 minutes 44 seconds)
* 2:42:38 (2 hours 42 minutes 38 seconds)
* 1:17:05 (1 hour 17 minutes 5 seconds)
* 36:40.91 (37 minutes 40 seconds 910 milliseconds)
* 17:40.34 (17 minutes 40 seconds 340 milliseconds)
Based on the length of the strings you have said that the ordering is 
incorrect, and I have confirmed, however in fact the order is OK, only the 
formatting differences are confusing. Based on this I am setting this bug as 
Invalid, as the sort by cpu time works ok, the problem seems the formatting. If 
you have any ideas, let's discuss them, I'll be happy to improve this upstream.

** Changed in: gnome-system-monitor (Ubuntu)
       Status: Triaged => Invalid

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https://bugs.launchpad.net/bugs/1026994

Title:
  Sort by CPU time is wrong

Status in The GNOME System Monitor:
  Confirmed
Status in “gnome-system-monitor” package in Ubuntu:
  Invalid

Bug description:
  The sort is happenning, but it looks like the processes were split into two 
groups (arbitrarily, as far as I can tell), each group being sorted 
independently. See the attached screenshot which is quite explicit.
  NB:
    - Sorting by increasing order still kept them grouped, with the 3-items 
group put at the end.
    - This grouping didn't affect sorting by any of the other columns I had set 
up.

  This is certainly not a major issue, it is just puzzling and could be
  an inconvenience if the first group was larger.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: gnome-system-monitor 3.4.1-0ubuntu1
  ProcVersionSignature: Ubuntu 3.2.0-25.40-generic 3.2.18
  Uname: Linux 3.2.0-25-generic i686
  ApportVersion: 2.0.1-0ubuntu11
  Architecture: i386
  Date: Fri Jul 20 10:44:27 2012
  InstallationMedia: Ubuntu 11.10 "Oneiric Ocelot" - Release i386 (20111012)
  SourcePackage: gnome-system-monitor
  UpgradeStatus: No upgrade log present (probably fresh install)

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