I have this problem with my system, initially I thought it might have
been KDE as I was using Gnome in 10.04. I later found that the same
thing occurred when using fluxbox so it obviously wasn't KDE related.
http://ubuntuforums.org/showthread.php?p=10032443 For me I found it
happened more when I had a virtual machine running (but it did still
occur when no VM was running.)

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Timer interrupt freezes, system becomes sluggish
https://bugs.launchpad.net/bugs/665796
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