Craig, that is really not helpful, though i suppose you may be trying to fool other readers. 
 
The issue is not bouncing of audio.    
 
The issue is bouncing of midi data fed to Kontakt to produce audio --- 'bounce to tracks' applied to midi tracks and their audio output tracks.    I have never said that I'm sure Kontakt is not at fault, it seems unlikely but certainly possible.      There are no other VSTs involved, there is no complicated routing, though there is an aux track with an ambiant reverb as part of the project.   All options are checked on the bouce dialog.  
 
Here's one more image, the same thing done twice the same way.  Same fairly large project.    It lines up perfectly, there are no changes that I can see anywhere.   It is exactly the same at the beginning as at the end -- 12 minutes long.     When I phase invert (using SoundForge ... don't know how to do it in Samplitude) and then combine the two, it is not silence but it is a much quieter version of the same thing -- THAT difference may well be some variation in the reverb or other peculiar different issue.  It is also possible that I'm phase-inverting a stereo track in the wrong way.   But again, it is NOT the very significant difference of the OP or of some of the other posts above. 
 
Work-around:   always do bounce-to-tracks exactly the same way.  Even if it might seem convenient to sometimes do an audible bounce and sometimes a fast bounce, don't do it.   Don't play bounced or frozen tracks alongside other tracks that are supposed to line up because they won't and don't.    Always sigh bounce everything all the time before listening, never try to bounce part and work with the rest, or freeze part and work with the rest. 
 

 
 

williamcopper
Craig, that is really not helpful, though i suppose you may be trying to fool other readers. 
 

 
Irony... meet head desk.
 
Head desk... meet irony.

Lol ... my response was to Craig's earlier post, when he illustrated that bouncing an audio track resulted in another audio track that looked the same.  

As to billing for mistakes ... I don't bill for anything these days, so CW needn't fear a bill in the mail.  But when I work, I work creatively, and that can include following false trails.    It's called being expert, imo.   Granted, I don't devote the time, effort, or the rigor of professional standards to this stuff ... if I ran CWs testing department, there'd be very little 'monkey time' spent -- cheap employees punching keys and yawning and scratching while they idly watch for a mistake.   There would be a complete set of testing scripts that automatically would handle all the initial and regression tests, over and over and over, and would store the results over and over in a database.   And I'd scour this forum for posts like this one.

Okay... so hopefully everyone watching can see how ridiculous this OP is. Don't let him/it waste your time.
 
cya...

Mr. Copper you don't bounce MIDI you convert MIDI to audio via a synth either hardware or software. Any result is due to the synth and its output. Bounce has a meaning and it doesn't apply to MIDI. 

williamcopper
Craig, that is really not helpful, though i suppose you may be trying to fool other readers.

 
Right. And to make sure people would be fooled, I provided all the details about the test and the methodology so that people could reproduce it themselves. Unlike you. 
 

The issue is not bouncing of audio.
 
The issue is bouncing of midi data fed to Kontakt to produce audio --- 'bounce to tracks' applied to midi tracks and their audio output tracks. 

 
 
Well, that helps, because your first sentence was [Italics mine]:
 
"See image.   Same music, slow bounce vs fast bounce.   While they align and sound similar, clearly they are not the same."
 
I took that as you were mixing down an entire composition of audio tracks, which were generated by bouncing Kontakt to create that audio. If you had been that clear at the outset, it would have saved me quite a bit of time. However, it's fortuitous you clarified that because in that case, I have a much larger body of data to draw on than the quick experiment I ran a few moments ago.
 
I just finished all the mixes for my new album "Neo-." These mixes have been done over a period of several months. I don't recall for sure if all the tracks used multiple instances of Kontakt, but many had five instances. In any event they were typically a mix of audio and multiple virtual instruments playing back in real time; some songs had tempo changes, some did not. Some synths and processors were upsampled, some were not; there was even a mix of 16- and 24-bit files, as well as looped and non-looped files. Some of the mixes were done using a real-time bounce because I wanted to hear it "one last time," and some were fast bounces because I was in a hurry. Some used the 64-bit engine and some didn't. In other words, it would be hard to imagine a situation with more variables.
 
I bounce all the tracks down to a final two-track within the project for reasons I've explained in other posts, so I won't go through that again. Typically, there will be four to ten bounces during the course of mixing a song, each with slight changes so I can compare them. Furthermore, I sometimes cut areas from one mix and put them in a different mix. As a result, I often hear separate bounced mixes play back simultaneously, and when deciding which intro to use, am zoomed way in on the beginning the tracks.
 
Throughout the entire creation of the album, no bounced mix exhibited a start time offset compared to either the original song, or the other tracks. 
 
 

John
Mr. Copper you don't bounce MIDI you convert MIDI to audio via a synth either hardware or software. Any result is due to the synth and its output. Bounce has a meaning and it doesn't apply to MIDI. 

You are correct, but here I'll give Mr. Copper some slack, because the function within SONAR you use to convert MIDI to audio is the bounce operation. I can see where he would be confused, and I was confused by his confusion.

I've edited the OP to clarify.   The operation that produces audio from a VST in association with midi tracks is called BY SONAR "Bounce to Tracks" ... Select Midi Tracks and VST Output Tracks, Select a time range, Track View - Tracks - Bounce to Tracks.    
 
Surely you'd not have me call it something else? 
 
Privately, actually, I call it "YO" .. because I've mapped a shortcut to solo all of a group of selected tracks as "Y" and a shortcut to use the Bounce to Tracks Dialog as "O".    
 
 
edit.   I don't generally use 'Freeze', because that involves a rather time-consuming unload of all the samples from Kontakt -- I have enough memory for what I do that this is not necessary or desirable. 

...aaand continuing to be just vague enough with just the right language to confuse newcomers/casual observers while still ensnaring those in the know into bullshiz, go nowhere conversations while COMPLETELY ignoring all legitimate advice, instructions and reality.
 
Yeah, Cakewalk owes you a BUTTLOAD of consulting fees.
 
lol

Come on Beepster.   I'll readily agree that I don't write well or clearly.  But help me out ... I think you know what I'm trying to show, why not say it clearly as you believe it might be better understood?