I have a single-core system, and as long as I run the calibre-parallel at Low priority my system hardly notices that a conversion is running. I am running windows 7 Pro as the OS rather than XP, so I guess that might make a difference.
I guess another variable might be RAM - if that got low it could push the system into excessive paging. I have 2GB on the system in question, so that is far more than Calibre ever wants to use.
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