The B3 in preacher mode appears to start and stop tones within one sample, making abrupt discontinuities in the waveform. It makes for clean, digital sounding and very annoying pops and clicks that I don't remember hearing from any real organ (admittedly I've never touched a real one myself, but there are lots of recordings of them). I don't know how, but the real ones seem to make much softer and nicer clicks.
Adjusting the attack knob helps a lot for the beginnings of notes, although it's tricky to get it set right. Is there anything I can do for the other end of the notes? There's no release knob anywhere.
I don't want to turn off preacher mode; it sounds too good :) Also, the chorus and vibrato do reduce the clicking, but I don't like them.