I recently got a new Thinkpad T500 with a duo core 2.53Ghz processor running Ubuntu Intrepid and was a bit annoyed that I was getting far more audio DIO dropouts in PD than my previous single core Pentium M 2Ghz Thinkpad T42p.
Last night I realized that the cpu frequency scaling was actually interfering and running both cores at 800Mhz while I had Jack and PD running in realtime mode! I had little to no dropouts on the T42p since the OnDemand scaling algorithm used by default only had one core to do the work and automatically bumped the cpu to max freq. With two cores it seems to think it can keep the freq lower and I get dropouts.
For those of you who might have noticed the same problem ("WTF! How can my NEW FAST machine be running PD like crap!!??!"), you can set the cpu scaling manually. Once I set my machine to Performance it bumped the speed to max and PD runs smooth as silk.
(I highly recommend this machine BTW, it is super quiet and super cool temperature wise. My previous Thinkpad feels like a hurricane toaster by comparison)