This seems to be a recurring issue that I have to deal with each time I reinstall linux on my laptops. The HD goes into aggressive standby / sleep mode every 3 seconds symptomised by a clicking sound every 3 seconds. The real problem is that it parks the HD head every 3 seconds. Not only is it a performance hit but apparently most HD's are only rated for 200,000 load cycles or something like that.

To verify you have this problem run 'smartctl --all /dev/sda' (where sda is your drive device). Look for (or grep for) 'Load_Cycle_Count'. Under normal running conditions this number should not go up. It might go up every time you turn off your computer or put it into suspend or sleep etc. so you'd expect maybe a few every day. If this number is going up every few minutes (or seconds), you've got this glitch.

To fix this glitch, turn off HD hibernation. i.e. '/sbin/hdparm -B 254 /dev/sda' for me. To verify the fix, look at the load cycle count again and it should no longer be incrementing like a freaking clock. Now the only thing you need to do is make sure that command is run every time the machine boots up, i.e. a script in /etc/rc.d/init.d (or be lazy and just put the command into an existing script which you know is run like cpuspeed).