Hard disk access makes GUI unresponsive

Hi,

 I'm running Feisty Kubuntu. I was recently running keep, a KDE backup utility that runs rdiff. I had it back up 10Gb of files from my main hard drive (contains home, root etc) to an empty one. This took about 30 minutes. Throughout this time, my GUI was very unresponsive. If I changed application, I would get an empty window at first and it would painfully load over 30 seconds or so. Scrolling would sometimes freeze for a few seconds too. Typing text into edit boxes would have delays of seconds between key presses. Doing anything new, like clicking the k-menu/start-button would take ages to happen.

 I have a dual-core CPU and rdiff was running at about 80% on only one core. I have 2GB RAM and had loads of memory free. hdparm says DMA is turned on for each of my drives. I reniced rdiff to 19 and it didn't make any difference. I would like the backup program to run every day, but it brings my system to its knees so bad that it's just not practical.

 What can I do to keep my GUI responsive when the hard drive is being accessed by rdiff? I don't understand why it hurts responsiveness so much, especially when hard disk access isn't required (e.g. switching to an already open app when I have memory free, typing in a box).

Would switching to the low latency kernel (the one for audio applications) help?

Any tips on how to diagnose the problem or things I could try would be appreciated.

Thanks.