I run PJ64 on a Dell Inspiron 8200 notebook with a P4 1.7 Mobile, 512 RAM, and an nVidia GeForce 4 Go with 64 megs and I too get this type of audio problem. Of course, it could be just the crappy, embarassed-to-admit, on-board Crystal Audio soundcard!
I have also noticed that even though I am running at full speed, the sound is not quite synced even with "sync game to audio" enabled.