try mounting ext3 paritions with "barrier=0"
this could be meta-bug with many things cousing performance loss.
it is fruther discussed here: 
http://forums.gentoo.org/viewtopic-t-482731-postdays-0-postorder-asc-highlight-fast-start-575.html

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System gets unresponsive under moderate load
https://bugs.launchpad.net/bugs/126274
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