I am affected too.. after an upgrade from 9.04.  Please see the attachment.
Have a look at the execution times of the same code (left terminal). It varies 
between 39, 45 and 57 seconds. The most often it is 57s. before the upgrade it 
was always 39. Please note the process distribution: CPU0 is almost not loaded. 
Also note the frequency on (bottom right) it is 2G not 2.66. 

Something else: When I change the freq by hand to "2.66" or
"Performance" or what ever it returns back to  "Ondemand" within several
seconds.

It is annoying... I do not know if it is the kernel or something else...

** Attachment added: "Screenshot.png"
   http://launchpadlibrarian.net/34700469/Screenshot.png

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Multicore CPU  Freqiency scaling broken
https://bugs.launchpad.net/bugs/462284
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