did you try disabling hal disk polling? you dont really need it since devkit is 
also polling every 2 seconds. i disabled mine by going to 
/usr/lib/hal/hald-addon-storage and renaming hald-addon-storage by placing an 
extra character at the end then rebooting. 
another thing i noticed is that i had a smilar problem and it was greatly 
reduced by reformatting to ex3 and installing on that instead of ext4. for some 
reason ext4 caused much heavier system lag during the periods of disk access 
every few seconds. if you dont mind not having a journaling filesystem you 
could always use ext2 and see how that works for you. honestly ive found ext2 
to be more stable for me and i dont mind the consequences of not having 
journaling. 

this problem may be related to these:
https://bugs.launchpad.net/ubuntu/+source/linux-source-2.6.20/+bug/75295
https://bugs.launchpad.net/ubuntu/+source/hal/+bug/85695
https://launchpad.net/ubuntu/+source/hal/+bug/27323

it's either a hal problem, a kernel problem, or both. no matter to me
though, i've noticed a similar set of symptoms on different computers
and these steps have always either stopped the problem for me or reduced
the severity of it to where the system is usable and the disk activity
becomes less frequent and heavy. it definitely extends the life of my
drives past what it would be with constant grinding.

-- 
kjournald2 writing to disk every few seconds
https://bugs.launchpad.net/bugs/483569
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