You could try some different method of capturing audio, like the one described here: Overruns with arecord at 192 khz 2 channel - #3 by Giedrius
Btw, the command shown (sudo jack_capture -p system:capture*) captures inputs directly. I think you should use instead sudo jack_capture -p system:playback* to catch the output after all the effects (or possibly no -p param might even be necessary)