Your screenshot answers a lot of question.
First that is not a file extension. That is a name of the wave file ...1.WAV  
 ....1 is what is is being named. 
And that is something like I get when I choose Tracks as the source. But I get Track 12.wave 
 
For source use Entire Mix. 
 
 
 

Cactus Music
Your screenshot answers a lot of question.
First that is not a file extension. That is a name of the wave file ...1.WAV  
 ....1 is what is is being named. 
And that is something like I get when I choose Tracks as the source. But I get Track 12.wave 
 
For source use Entire Mix. 
 

I've been using "main outputs" for source since Sonar 6 came out, which is when I started using Sonar, without an issue until now.


 
I just checked, and it defaults to both files to start with. As well as Entire Mix. So it makes no difference.
 
It's just a couple of extra mouse clicks -- not exactly a hardship. But it seems odd that it should start behaving that way.