For a substantial project, midi controller "look-back" does not work outside of a certain time or measure length.   Therefore, beginning work somewhere in the middle of the project gives false readings.   When you later come to render the midi, you'll get a different sound than that you had worked over.

Solution to this one would seem easy:  whatever the limitation to look-back is (time, ticks, bars, samples) ... make it an option to look-back all the way to 0. 

You should put in a feature request.

- Steps to reproduce?
- What controller number(s)?
- What synth(s)?
- How many measures?
- Does it matter how many other tracks are in the project?
 
 

Any controller, any number of tracks --- seems to be entirely a matter of duration.   Not sure if the duration is in measures or clock time, but it's around 1 minute I believe.   The 'signal' to tell it's happening is the controller shadowing in PRV controller pane disappears.   For Patch Changes, there is no shadowing but I'm pretty sure it happens the same way. 

I'm pretty sure it was discussed here already.

Adq, it was discussed and generally dismissed as not a problem --- the thing is that it IS a problem.    If you render midi beginning partway through a project, you will get a different result at the relevant place in time than if you render midi beginning at the beginning --- and this bug is one of the reasons.  
 
For large and complicated projects, it is not at all easy to identify what is going wrong -- so: yes, a bug; yes a problem.

This is the Problem Reports forum. Discussion is not going to cut it. The idea is to give a reproducible recipe, have others confirm it if possible, and then enter a formal Problem Report based on that recipe.
 
Since none has been given, I tried to cook up my own:
 
I put MIDI clips in two tracks, one hardware synth (Aslesis QSR), and one soft synth (TruePianos) at measure 1001 (32 minutes at 125BPM). Then I went back and inserted CC64=127 sustain controllers at 1:01:000 in both tracks. I have Zero Controllers on Stop and Patch/Controller Searchback enabled. For good measure, I enabled input echo on the MIDI tracks and cycled my sustain pedal to ensure both synths got a CC64=0 before playback started.
 
I started and stopped playback several times both before at the beginning of and in the middle of the clips, and both synths played every note with sustain held throughout with Zero Controllers stopping the sustain on stop as expected.
 
As I suggested earlier, it appears to me that the lack of a controller shadow is a display issue only; the last controller value is still in force, and searchback seems to be working fine as well.
 
So we're back to square one, Gentlemen. I'll be happy to try and reproduce any detailed steps you care to submit.
 
P.S. Since William has mentioned Kontakt previously, I just tried the above with Alicia's Keys in Kontakt Player, and it behaved properly as well. I don't have the full Kontakt sampler.
 

Put in a change of the controller at bar 200; ensure it is far enough out that the controller shadow is gone; ensure that the end time is far enough out that the bar 200 controller shadow is gone.    Render from beginning, and then from after the bar200 controller shadow.   The recent issue for me was in fact a patch change, so exhaustive tests might include CC1, CC7, CC11, the patch change CC#s (? don't remember them offhand) and then some unusual controllers, just in case Sonar handles them differently.   This is most likely a sonar bug, nothing to do with Kontakt -- though Kontakt has its own bug with handling controllers sent to an instrument that is part of a "Bank" and not part of a "Multi". 
 

Hold the phone. Looking back, I see you're talking about rendering, not playback. That makes me think the issue is that you're not including the controllers in the selection. Searchback only applies to playback. I think it would be a feature request to have Searchback include rendering the effect of non-note events that aren't included the selection.
 
EDIT: Cross-posted. I see the problem now. Call it a bug if you wish, but bouncing was never intended to include events that aren't selected.