I have the similar problem- Juk 2.0.1 Kde 3.2.3 I use gstreamer and kernel 2.6.6 with the preemptive patch and deadline scheduler. I have set x's nice value to 0 and arts gets a little improvement, but it still distorts the sound. If i use gstreamer, juk's gui will freeze between songs for at least 10 seconds (even up to a minute).
I've reported this bug to bugs.kde.org - bug # 86810. Thanks, James