I have the same problem. My sound card is Integrated into my ASUS motherboard -- it is a Realtek HD Audio ALC882. I have popping sounds that occur with a frequency proportionate to the buffer length specified in the plugin. If I turn on the "sync game to audio" option, I have a block of sound, *pop*, an equally long block of NO SOUND, *pop*, sound, *pop*, no sound.... and so on. The game also stutters with each pop in this mode. As of right now, It is much more playable without the "sync game" option, but it still is annoying me.
Even stranger: several times (seemingly at random) the sound completely cuts out of a game, usually at a loading point, and then does not come back. Ever. Nothing fixes the problem except restarting the ROM (F1-Reset, or F12-Stop and then starting it again). Interestingly, If i do this, it will eventually go away again, and so I find the ultimate solution to be to restart PJ64 as a whole.
