The system is AMD Duron 700Mhz, Win XP pro, 384MB RAM, GEForce 4 AGP4x 64Mb, VIA chipset , VIA audio.
I don't know how to tell which audio plugin's I am using.
Well, you can read the help to see how you switch plugins. Tell which one you're using and try experiment a little. You never know if you might solve it on your own.
Try using 1964 0.9.9 as well, because when your processor is below recommended requirements, the game speed may be fine but the audio takes a hit and becomes choppy. 1964 0.9.9 is a faster emulator, so perhaps the sound will be better.
I recommend using Azimers HLE plugin (preferrably .55.1 or .40 beta 2) (edit: too bad there isnt gonig to be another one, oh well), I think they perform better than the rest, however Jabos and Schibos are good too.