timidi
Never thought of muting the master to check for missed routings. That's a great idea. 
 
I do sort of what johnny does. In that, I do bounce to track just using the default. Seems to work.
Then, if taking the resulting wav out of Sonar, I just drag it out to wherever. Usually the desktop and then organize from there.
 
That said, I don't think I understand your question Batsbrew.
If your busses are routed to the master they shouldn't be occurring on the main out except through the master.
 

well, that's what i always thought too...
 
if busses are routed to master.  
 
but in the dialog box, for selecting the sources and outputs:
 
In the Source Category field:
 
Main Outputs. Choosing this option creates new separate tracks for each main output you highlight in the Source Buses/Tracks field. Each main output you highlight will produce a new mono track, stereo track, or two to eight new mono tracks (the Split Mono option), depending on whether the output is a stereo output or the Surround Main, and depending on what you choose in the Channel Format field.
vs
  
Entire Mix. Choosing this option bounces your entire mix down to a new mono track, stereo track, or two to eight new mono tracks (the Split Mono option), depending on whether the output is a stereo output or the Surround Main, and depending on what you choose in the Channel Format field.
 
so i've always chosen 'entire mix'
 
but, wouldn't the purist way to do it, be to simply output from the mains?
 
assuming that all the automation and fx, etc, are always active routing thru the mains?

one reason i like to bounce the entire mix down to stereo file in the same project,
is so that i can solo the new final mix track, routed directly to mains,
against the original mix with the new bounced track muted,
and verify that the actually sound the same.
 

well.
 
after 6 attempts at exporting final mixes using 'mains' as the source,
i definitely am not getting what i should be getting.
 
and do not know why.
 

Still not quite sure what you're asking Rob, but; are all your tracks either routed to a bus or to the master bus, are all the busses routed to the master bus, and is the master bus routed to the mains?
 
 

of course,
all tracks are routed to busses,
and all busses are routed to master,
and master is routed to mains.
 
i want the mains output.
something is wrong internally with the routing.
 
again, i'm on sonar 6 PE

Do you perhaps have another, hidden Main, such as for a headphone mix?

nope.
it's all clean as a whistle.

Gregs point is a good one. I was going nuts once wondering why my exported wave showed overs in Wave Lab even though I had the Brickwall limiter set at -.4 All my exports always reflect this setting. If they don't , then something is not going through the master. What is was was exactly what Greg said and I had to use the Track View thing and saw there was an extra buss unchecked so you don't see it. So there's another place to look. 

doesn't select all take care of that automatically?
 
does it really NOT select all?
 
i don't have any busses not being used, how could a missing buss occur?
 

Well not sure about Sonar 6 anymore, But example is my hidden buss seemed to be created by using a track template. Inserting a track from a certain template I use for Bass also seemed to insert a new master buss which for some weird reason was hidden. What I noticed was the word Master said master in the bass tracks output? Why no capital?? Then a light buldb went on and I opened the Track Manager and found a second buss which if they are not ticked the don't show. This sometimes happens in the tracks as well and you'll see a missing number , like there's no track 6. So I  have often remembered to open the Track Manager to find a missing track. SO not sure if Sonar 6 has a Track Manager, been a while.