Hi All,
 
I have that problem for a while and can't solve it. 
 
I have project with multiple midi tracks+vst, I am using komplete kontrol keyboard. 
 
As usual I am setting up Input as my Komplete kontrol - omni  ( it only works on Channel 1 or Omni but that doesn't fix my problem)
So all my tracks have the same input setting. While playback, everything is fine, until I want to bounce all tracks. 
All my Midi tracks play on one of the other tracks. Let's say I have Piano, Bass, and drums. 
Then Bass and drums will play on Piano track, it seems to be random and only when bounce to track.
 
I started happening like 4 updates ago. 
It's really annoying as I have to bounce single tracks to audio and then bounce them together. 
 
Anyone ? 

When you say " until I want to bounce all tracks. 
All my Midi tracks play on one of the other tracks." do you mean the bounce mixes them all together into one audio file on one track?
 
Does the same thing happen if you "freeze" the tracks?  

Yes, that means when I want to bounce mix them all together. 
I don't really use freeze option, but I think it won't because freeze is nothing else like bouncing to audio. 
 
It's probably easy fix but it drives me insane. 

Fast bounce or real time? If real time, I'm thinking possibly the Out on your keyboard is acting as a Thru and echoing everything to the currently focused track. But I'm not sure how that would only happen during bounce. In any case, try disabling Always Echo Current MIDI Track in preferences, and manually disable input echo on the Piano track.
 
If it isn't the keyboard echoing MIDI Out back to the MIDI In, I would suspect maybe a virtual MIDI cable app being involved.
 
And just to confirm, the instruments are different synths, not a single multitimbral VSTi...? 
 
Incidentally,  I would recommend you always set inputs to a specific channel, not Omni, to avoid problems like this in the future, even if it's not the cause now.

It's fast bounce, but I tried real time bounce as well with same issue. 
 
It's different Synths, my habit is, I create new synth new instance of kontakt etc. and they are all on the same midi channel. Probably you are right, would be good to set them on different channels and that also would solve the problem I think. 
 
I forgot about auto echo current track,  I think that also will solve the problem. 
 
I think it's time to get rid of bad habits. 
 
Thank you for suggestions. 

Uneasy
Yes, that means when I want to bounce mix them all together. 
I don't really use freeze option, but I think it won't because freeze is nothing else like bouncing to audio. 
 
It's probably easy fix but it drives me insane. 

Freeze is EXACTLY the same as bouncing to Audio
 
What is it that makes you think otherwise?

Bristol, Does freezing actually create a .wav file for the audio?
 

Yes, freeze and bounce both render wav files. The main differences between freeze and bounce are:
1) freeze reuses the same track where bounce creates a new track to host the rendered wav.
2) freeze bypasses the FX Rack and ProChannel after rendering
3) freeze disconnects the synth, if any, after rendering
The risk with freeze is accidentally unfreezing the track. Usually this is only a problem if there has been some additional work done to the track after freezing such as additional editing or re-enabling the FX Rack or ProChannel for post-freeze FX processing. Unfreezing restores the original wave and enables the FX Rack and ProChannel but does not restore the FX Rack and ProChannel to the state before the freeze. When it is necessary to edit a frozen track copy the audio to a new track and work on it there.