I export audio when I am done with the mixing. I always select only the master buss. Doing this, one needs to rout all tracks and buses to the master buss and do not select anything. Select the the master buss in the export dialog. It is completely fool proof and consistent. 

BENT
FWIW, I think it's a good idea to bounce all tracks to one clip in a new track first, top and tail it with an automation envelope and then compare this new audio track against all the others. If you slipped up somewhere you will hear it before exporting.   

That sound like a good idea. Never knew that feature existed :-)
How do you bounce all clips to a new track?
 
Edit: Never mind my question on how to bounce. Just found the menu.

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That sound like a good idea. Never knew that feature existed :-)
How do you bounce all clips to a new track?

Exactly the same way you bounce one single track, except for selecting all (active) tracks instead of just one.

Well, just tested the bounce to tracks.
But it does not work either.
 
I think I found out what is the problem: Sonar neglects to take care of my automation, which I have on the track (on CCs and on volume). It seems to pretend, that I have no automation. Even though I have checked all "Mix Enables" like "Track Automation", "Bus Automation", "FX Synth Automation" and all the others.
 
The strange thing is: It works fine, if I play it live. The probelm first appears if I bounce or export the audio.

Weird, assuming you do have "Automation Read" enabled on all tracks, and that you are not in offset mode (do you see "+"'s in the track headers?)

Alatar
I think I found out what is the problem: Sonar neglects to take care of my automation, which I have on the track (on CCs and on volume). It seems to pretend, that I have no automation. Even though I have checked all "Mix Enables" like "Track Automation", "Bus Automation", "FX Synth Automation" and all the others.

 
Maybe you missed my comment above: "Fast Bounce is essential when doing MIDI projects with automation." Try using only fast bounce. This is actually a better option because it never fails to allocate sufficient resources for the bounce. With a real-time bounce, there's the possibility of dropouts and other issues if there aren't enough sample buffers.

Some good tips on final mixdown here. Maybe they could end up in the Tip of the Week.

Back from the dead!
 
Did you ever find a solution to this? I just had the very same problem. Ive been using Sonar for a very long time and this is the first time its ever done it to me.. I just ended up bouncing the tracks to bypass the bus automation. Would love to know what I (apparently) changed / did to cause this?