I may be having a similar problem.  Periodically throughout the day, the
hard drive is vigorously accessed.  My CPU usage does not increase to
100%, but some processing is going on.  Running "top" from the command
line doesn't reveal any obvious suspects and I have scanned through the
complete process list to no avail.  I wonder if Firefox might be working
with its cache or something, but that's a long shot.  I do not have
tracker installed and there is no indexing going on.  Any ideas?

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Ubuntu 8.04 : after installing april 8/2008 updates, hard drive led never stops 
flashing and CPU consuption is VERY high
https://bugs.launchpad.net/bugs/214763
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