I have been experimenting a lot with audio on Lubuntu 12.04.
On the laptop I use the internal sound card with alsamixer,
and there are no issues with jpskmail 2.0.x.
On the new 4-core desktop machine I use pulse audio,
and I have spent hours to get the DSP to decode properly.
First it looked like an audio level problem, and it was very
difficult to set the levels correctly. Until I noticed that the
waterfall looked different when I was running pavucontrol,
the pulse audio level controller...
It turned out that when I leave pavucontrol running, the problems are gone.
Levels should be set to 'base' on the input device and 100% on recording.
Obviously pulse audio is not running in real time when it is used
by alien (java) applications, and it feeds the DSP with undefinable chunks of audio.
****You have now been warned.... :-) ****
By the way, jpskmail-2.0.13 uses only 6% CPU on the new machine....