There were some early bugs in Dapper relating to memory usage problems... which appeared to be IO problems, mainly because it was trying to cache the whole hard drive and then some into memory and was also trying to not swap out to kep it fast...
So, the question it, are you running Dapper, Edgy or Fiesty?
If Dapper, is it up-to-date?
If Edgy... I dunno.
If Fiesty... you are on you own.
One question, do you have hdparm installed? And Tweaked for the drives?
For you info, I am running Dapper on my laptop it is an 800MHz, 512MB RAM, ATA66 Hard Drive @ 5400RPM.