I've never had this trouble before. I am recording my entire project to an audio track by routing back through my mixer, like I always do when my project is done, only this time I'm getting little mid-range pops here and there. The levels are plenty low and sane, and anyway, the pops don't happen at peaks. I've tried twice and got them both times, but in slightly different places. All tracks are frozen or were audio. There are EQs on most tracks, and a couple reverbs and gates. About 40 tracks in all, though only about 20 are playing at a time. I don't hear the pops during playback or while doing the actual bouncing, it only appears in the resulting wave.
 
What might be causing this?

Have you tried raising your buffers?
 
One explanation for why pops occur when you go out to the mixer but not during normal playback is the added latency incurred by the ADC re-conversion coming back in. 
 
 

Addendum to bitflipper's post, "Number of Buffers" and "Prepare using nnn Millisecond Buffers" can be found in:
 
Edit/Preferences->MIDI->Playback and Recording
 
My values are 64 and 500 resp.

jkoseattle
I don't hear the pops during playback or while doing the actual bouncing, it only appears in the resulting wave.

That's pretty strange. If accurate, I think it would have to mean the error is occurring as the audio data are written to disk.
 
You might try temporarily moving the project to a different drive if possible. You might also try changing the disk record buffer size or enabling/disabling Write Caching (Preferences > Audio > Sync and Caching > File System), depending on whether you've altered anything from the defaults.

I don't understand why you're converting the output to analog and re-converting it back to digital through your mixer to end up with a digital WAV file of the final mix.
Wouldn't it be much simpler to just Export the the project mixdown direct to a WAV file (which you can import back into Sonar if you want)? This avoids the extra and unnecessary latency of the DA then AD conversion. I agree that pops are most likely caused by buffer size/number of buffers. See if the pops get further apart as you increase buffer size.
 

If it's only happening on mixdown, try disabling fast bounce.
If the resulting mixdown is free of pops and clicks, it is likely that one of the plugs you have running in the project does not like fast bounce.  You have to go hunting for the offending plug, rinse and repeat.
 
I had this issue but it was a multi sample flatline once at random points in the song upon fast bounce mixdown only. Turned out to be a plug.
 

rjeynes
I don't understand why you're converting the output to analog and re-converting it back to digital through your mixer to end up with a digital WAV file of the final mix.

Some people prefer the sound of analog summing. And normal record latency compensation will take care of the round-trip latency.

bitman
If it's only happening on mixdown, try disabling fast bounce.

Hey Ron, he used the term "bounce" in the title, but the description indicates he's just recording the analog signal coming back from an external mixer in real time - i.e. old school 'bounce'.

Oh.
 
K.