This is very strange!!!  I just started a new project, and I get weird rhythmic crackling on the off-beats, which is when my organ part plays. 
 
- I'm using Kontakt 5 for my sounds, which is my usual soft synth. 
 
- The organ sound in question is called "Equinox Change" which is a "showcase instrument".  If I change to a different organ sound, the crackle goes away.
 
- The Equinox Change sound has a "Chord" setting.  By default, it's on.  If I turn it off, the crackle goes away.
 
- If I solo the bass sound, I still get the crackling on the off-beats where the organ would play (even though it does not play). 
 
- If I mute the organ track (or move the organ clip to a later measure), the crackling goes away.  So, for some reason, the presence of un-muted organ notes causes crackling, even if the organ sound itself it not audible.
 
- The crackle is the standard pops and clicks sound which you get when you have latency set too low. 
 
- Increasing the latency helps a little, but even if I increase it to 256ms and higher, I still get some crackle.
 
- I have tried 2 different sound cards: Focusrite Scarlett (ASIO) and M-Audio Delta-44 (ASIO and WDM).  Both give me the same crackling sounds at the same places.
 
 
So, it looks like the "Chord" feature in Kontakt is creating the crackling sound in Sonar.
 
Any idea how to fix it (aside from turning "Chord" off for certain Kontakt instruments)?
 
 
 

It sounds as though that particular Kontakt sound might be a resource hog. Muting a soft synth does not stop it using resources - only disconnecting or freezing will.

It would seem that this is a question for the Kontakt people obviously a bug in this patch. 
Myself I would just move on, I have little patients with things that don't work and I move on to what does work. There are certainly many great organ patches around. 

Bounce the organ part to a track and unload it.
 
Dan

Is there:
1. A tempo change at the spot where crackles happen?
-and-
2. A tempo-based effect either on the tracks/buses carrying those voices -or- built in to the synth voices

Actually, it happens with the standalone Kontakt as well (outside of Sonar).  It seems to be dependent on how many notes I play; the more notes that are pushed at the time the "Chord" feature is running, the more crackle there is.

Tripecac
Actually, it happens with the standalone Kontakt as well (outside of Sonar).  It seems to be dependent on how many notes I play; the more notes that are pushed at the time the "Chord" feature is running, the more crackle there is.

OK, that does sound like what happens when buffers aren't big enough to support the CPU load of many notes. But you said you could not get it to go away with 256 ms, which is pretty big. (ms, not samples, right?) Also, does task manager say you are near 100% CPU continuously when you are playing these notes & chords?