Hi ..I'm having the same problem as discussed in this issue. I use Toshiba 
laptop (MK2552GSX 250GB hard disk) and having the same problem of hard disk 
getting overheated even when no significant I/O activity on the machine. I have 
dual boot on my machine and could confirm this problem is specific to ubuntu 
and not in vista. When i approached Toshiba service centre, they mentioned to 
me that they heard more problems like these from other Toshiba users who use 
ubuntu 9.04 or 9.10 as their OS
and they said they can't do anything about it as they support only vista. 
Someone from Ubuntu should seriously look in to this.

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HDD unusual high temperature and activity in Ubuntu Jaunty
https://bugs.launchpad.net/bugs/394826
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