I had this strange behaviour too.

On a MB (GA/nforce560) I used a Seagate 7200.11 (SATA) and a fresh install of 
Ubuntu 8.10.
I noticed a HDD activity every 4-5 sec, which was very annoying.
Because of the Firmware bug of the Harddisc I decided to replace the HDD with 
another one.
I took a Seagate 7200.10 (IDE) and never noticed this problem again.
-> so the problem seems to be caused by something SATA-related (?)

But it became more crazy: After flashing the firmware of the 7200.11 I put it 
into another
PC (GA/nforce3-150) and also did a fresh install of 8.10. The problem did not 
occur on that system!

So in  my thinking the cause of this problem is:
- either the firmware of the hdd (cache flush?)
- the driver or some driver related software of the nforce560 sata controller

I hope this can help you locating this effect.

-- 
hard disk being accessed every 4 sec.
https://bugs.launchpad.net/bugs/17878
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