System unresponsive during HDD activity

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  For some reason, while running HDD-intensive tasks (e.g. svn update on 
a large tree), system becomes extremely unresponsive.
And I don't mean tasks that require any disk access - I'm trying to type 
inside an ssh session in a terminal, and the remote machine is getting 
my keystrokes after a pretty long delay.

Just now, composing this email, thunderbird got stuck at the previous 
sentence for a second while it was downloading new messages.

What's going on??

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