How much physical RAM do you have? If you have too little <512MB then the system will use the HD as extended RAM so if it has to do that a lot and you are also using the HD a lot for other things then you will get a slow down. Copying from one HD to the other on the same IDE channel will slow down access to other things on that channel but it shouldn't slow the system down because if there is enough RAM it won't need to be accessing the HD all the time.