I don't know when this started as I haven't done any mixdowns for the last couple of months. 
However, today I've done two mixdowns (bounce to tracks) and the stereo Left track is lower volume level (approx. 3DB)  than the right track.  They both should be the same (I'm bouncing mono tracks).  I didn't notice this on mixes I've done (since I got Sonar 6) and I'm doing it exactly the same way (using defaults in the Bounce function). 
 
I'm using the latest Sonar Platinum version (2017.01).  I rolled back to the previous version and did a mixdown and the same thing.
 
My recording interface units are not the problem (the mixdown should be strictly a Sonar function).  Just in case it was, I used my backup unit and it did the same thing.  My primary is a MOTU 896mk3 Hybrid and my backup is a Focusrite 6i6 2nd generation.
 
I had marked this solved but the problem showed up again today. 

Lemmie axe you dis:
 
Are you measuring the difference, or perceiving it?
The reason I ask is this. If the sources are the same audio but out of sample sync, the first arrival at your ears will sound louder than the later one.

I can see it, looking at the waveforms in Sonar and in Goldwave.  I can also see the difference in the level meters for both channels. 
 
I got around it, for these two mixes since they are all mono tracks, by mixing down as mono instead of stereo and then converting to stereo in the track.  Both left and right are identical that way.

It could depend on what's being specified as the source, for example, if the panpot on the Master bus is misadjusted.

Bouncing to tracks will generate a +3db bump if you use the default pan law. I ran into this and changed to another pan law to correct it. 

The panning is set at "0" (center).  I've done a ton of mixdowns this way before and never noticed any difference in the two channels.  The session template I used was one that I used on previous sessions.  
 
I went back and looked at some older projects and the two channels are equal on them.  Only difference is the version of Sonar.  I'm off for a gig tonight.  I'll try rolling back tomorrow to a couple of months ago version and see what it does.

If you read the help files it states that the default pan law "0" (center) will add 3db to anything that's panned hard left or right when you bounce to tracks. I think Sonar is seeing your mono track as a hard panned stereo track when it's bounced to a stereo track. Try the pan law at the bottom of the drop down list in preferences, I think it might fix your problem.

I not familiar with your I/O - but anytime that happens to me it is because I have multiple outs on my I/O and I have left the headphone or another aux volume up/open.  You can't hear it in the master out, but it does get included in the mixdown.  Just a thought...

Rolled back to 2016.09.  Did a mixdown with one of the projects that mixes with the left channel lower than the right and NO PROBLEM - both channels are the same level.  Using the same defaults in Bounce to Track(s).
 
I guess I'll have to start from the 2016.09 and try each monthly upgrade to see where it goes off.
 

Well, the problem went away!  I rolled back to 2016-10, 11 and 12 and it was all OK.  I installed the current version, which had the problem and its gone.  However, after I first had the problem, I rolled back to 2016-12 and still had the problem.  I updated to the current version and it too was still there.  That was when I first posted about the problem.
 
Only conclusion I can think of is one of the older versions reset/cleared whatever the problem was.  I did the mixdown (Bounce) the same in every version (and the same way I've done it for years).  ##@!%^%