There are so many terrible crackle noises when I tried to dither and export a 64bit floating point processed master audio into 24bit and encoded into FLAC file from SONAR. I thought that's because my audio gears, so I'd tried to clean all of them, but nothing helps....
 
So I decided to look into that flac file then I found those crackle sounds inside:

 
 
 
 
But when I tried to dither into 16bit and encode into FLAC from SONAR, no any crackle problems.
 
And so next, I tried to export the dithered 24bit result into wav file, and then encoded into FLAC by my own FLAC 1.3.2 codec downloaded from FLAC official website, all things are alright and no more crackle sounds finally!!

 
 
So you guys can compare about the crackle sounds from waveforms above at the exactly same sample positions....
 
And I found those crackle sounds appear only when I encode a 24bit result with final master clippings into FLAC.
When I encode a 24bit result with absolutely no any clippings or even no samples are all 1, all things are alright and absolutely no more any crackle sounds from the FLAC output.
 
So let me make a simple conclusion here:
Dithering 64bit into 24bit FLAC with clippings in SONAR: so many terrible crackle sounds.
Dithering 64bit into 24bit FLAC with all sounds below 0dB in SONAR: no crackle sounds.
Dithering 64bit into 16bit FLAC with clippings in SONAR: no crackle sounds.
Dithering 64bit into 24bit wav file with clippings in SONAR, and then encoded into FLAC with my own FLAC 1.3.2 codec: no crackle sounds.
 
So...... would it be the time for SONAR to stop using its "libFLAC 1.0.26pre5 20141125" and upgrade its FLAC codec into the latest up-to-date verison 1.3.2? 
 
 
My config:
SONAR platinum 23.4.0.38
Magix (Sony) sound forge 11 build 345
Windows 10 pro 1703 x64
Echo AudioFire 4
Nectar Impact GX61
Intel 2600

Maybe my English is not enough and I understand something wrong.
Why is a "Master" clipped ?? We master for clients. The loudest peak is -0,2 dB.
No Master, no track, no bus maybe clipped or reach 0.
Therefore the FLAC-Converter must make nonsense if he had to convert clipped audio. That is no Bug. 

If the master bus is clipping then you are going to get crackling because the clipping gets converted/output along with everything else.

The master bus should never be allowed to go over 0dB.

no internal track/bus/rendering/inter-plugins clipping i meant, i use 64bit FP from raw clips until the final down sampling, so clippings are only occurred when dithering down sample bit size.
 
I don't think there are any problems while clippings in the really final stage to CD, as well as the most popular music albums today globally let some of their drums clip a little bit, like linkin park, Michael Jackson 2000s collections, etc........ some of a little drums should clip a little bit in the final stage for me, which well in controlled.
 
So sorry but my 16bit version of the same clipping track does not contain any crackle sound inside, whatever by listening or searching inside its waveforms. there are no crackle sounds as well even in my 24bit wav file version and the 3rd-party FLAC 1.3.2 version, if you guys really know reading the waveforms i've shown above and read those crackle locations at the exactly same positions....
 
So common senses tell us those crackle sounds are not from my original clippings........ maybe you guys still have not read my post completely yet...........
 

Dithering 64bit into 24bit FLAC with clippings in SONAR: so many terrible crackle sounds.
Dithering 64bit into 24bit FLAC with all sounds below 0dB in SONAR: no crackle sounds.
Dithering 64bit into 16bit FLAC with clippings in SONAR: no crackle sounds.
Dithering 64bit into 24bit wav file with clippings in SONAR, and then encoded into FLAC with my own FLAC 1.3.2 codec: no crackle sounds.

There are a lot of problems if you do the final stage to CD with clipped audio.
In the second graphic there is a broken waveform by 01:22.170 and a distortion by 01:22.180
We have 15 years experience with digitazing tapes and vinyl. Also with mastering AudioCDs for a lot of clients.
OK - there is no crackle - but THIS waveforms will result as crackles by a lot of CD-players. You should also never reach 0 dB, because a lot of CD-Player crackle by reaching 0dB.
Our company has also ripped over 50.000 CDs to harddrive for a lot of consumers for example for the German National Library. We know the specifications. But I'm limited in writing and reading, because I must translate german into english.
 

I think the "bug" is in your file handling, not the conversion process. I opened up the waveform and enlarged it. You say the waveforms aren't clipping yet even if the clipping is intentional, the waveform is hitting 0. Conversion processes sometimes need headroom.
 

 
Normalize your "masters" to -1 dB and see if the crackles still occur. Then if you want a higher level, normalize the converted file to -0.1. BTW if you submit a master that hits 0 for more than a certain number of samples, most CD duplication houses will reject the master because they assume that hitting 0 means that clipping has occurred.

The fact that you get unwanted artifacts ONLY when dithering from 24 bit into the same encoder seems to point to a code error...it is obviously a math issue because dithering the same clips 16 versus 24 gets different results...

My guess is you are correct and Sonar probably needs to pay more attention to FLAC than they have in the past, typically home studios do not really do the majority of their work in FLAC but it is becoming a defacto standard in future proof studio environments...24 bit lossless high Khz recordings are becoming standard sub genres in almost all the places I work with...so a little bit of code tweaking might be in order here.

Frankly it seems a little odd to me that you would get crackles at 24 and NOT 16, that seems backwards dithering at 16 bit give you LESS headroom than dithering at 24 bit...I am not convinced its a code issue unless you can replicate it on another project...anomalies happen.

By the way, there is absolutely no reason to have clipping in a DAW, its just bad form...Sonar (and about a hundred other vendors) offers a decent limiter...it's there for a reason...

SONAR gets its FLAC implementation from LIBSNDFILE - we don't include FLAC directly. I see some updates for FLAC from LIBSNDFILE. Can you download the latest libsndfile DLL from their site and see if it fixes your issue?
You can download it here http://www.mega-nerd.com/libsndfile/#Download
The latest from there is Version 1.0.28. You should be able to replace the libsndfile-1.dll file in the Cakewalk programs folder with the newer one and test.

I thought every sound engineers should know how to read waveforms but it seems like I was wrong......... 
For clippings leading to other troubles than flac encoding, they are another matters. I will deal with but not now this stage. I can fade down the level of Izotope limiters, change the limiting rules or make them soft-clipping (round-angle clippings) or more and more other ways. So it's not necessary to worry about that for me, I know the Pope is Catholic and Paris is in France of course. 
 
Only Psychobillybob here is the smart one and really understand what's the problem I described. the same clipping track is completely alright when bouncing into 16bit flac or 24bit wav file, and encoding by FLAC 1.3.2 is completely alright as well. I can't imagine how complicated would the topic be.......
 
 
And I can't understand why today 2017 SONAR is still using the testing version "pre5" of FLAC (or something like beta/alpha versions) and not any stable versions of FLAC like 1.3.2, 1.3.1 or previous.........
I think v.1.0.26 of 25th Nov 2014 is an antique FLAC version.........

Noel Borthwick [Cakewalk]
SONAR gets its FLAC implementation from LIBSNDFILE - we don't include FLAC directly. I see some updates for FLAC from LIBSNDFILE. Can you download the latest libsndfile DLL from their site and see if it fixes your issue?
You can download it here http://www.mega-nerd.com/libsndfile/#Download
The latest from there is Version 1.0.28. You should be able to replace the libsndfile-1.dll file in the Cakewalk programs folder with the newer one and test.

 
just tried, replaced with the April 2017 1.0.28 one, and the FLAC tag shows "reference libFLAC 1.3.2 20170101" now, but nothing helps....... the same crackles are still existed......... 
Strange...... all things are going alright while I bounce 24bit wav file then encode into FLAC by myself.........