Ok some people have a northbridge chip on their motherboard. If so you could be getting some memory lag due to the chip getting very hot.
Since I Started using this program I have seen alot better responce time out of my machine
Cools your drives down also;)
http://www.almico.com/speedfan433.exe
Heres the main site for what the program does
http://www.almico.com/speedfan.php