The popping seems to be a problem with "Java Sound Audio Engine".
I added a menu to allow users to pick a playback path. Even with Windows, the "Java Sound Audio Engine" is causing popping, but the "Direct" options work fine. I'm not going to try and debug the JSAE, as it is easy to avoid and higher performance "direct" path.
The fellow helping me troubleshoot the JTheremin on his Linux system said that selecting ALSA "direct" lines worked. He was also getting the clicking due to the program defaulting to the "Java Sound Audio Engine". Maybe you can get some improvements by making sure you aren't using this engine as part of your audio path.
Some interesting info on various sound cards & drivers:
If you are curious, you can run the Applet and press Option, it should display your playback options. Also, the incoming options (for sound capture) will be shown on the Java Console, as well all Ports. The routine which builds the menu options goes through ALL Java "Mixers" and either puts them in the menu option group or "rejects" them to the console.