Jerks only when connecting RAID on different controllers

Hello,
I am trying to connect my two new hard disk (2 x Western Digital 160gb ATA100 7200rpm 2mb - OEM) to my on board raid controller on my KT3 Ultra boards.
If I connect them on the same IDE cable to controller 3 then they work fine.
However if i connect them to different controllers (3 and 4) then my PC will stop responding for a couple of milliseconds every minute or so.
Should they work better on different controllers?
I've updated all my drivers and bios.
I run windows XP on an AMD XP1900+, 756mb Ram, Geforce 4 ti4200.
I also have two older 80gb disks connected as master and slave to controller 1 and a DVD drive and CD drive connected to controller 2.
Any suggestions would be greatly appreciated
Kind regards,
Matt Jordan

ahh...
I tried setting them up as masters each but they werent being found. I then changed them to both being slaves and they worked. But that was while it was giving me that problem.
So do I just need to set the to stand alone by taking the jumpers off?!
Thank you very much
Matt Jordan

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