I have Sonar X3 Producer.  When I bounce my tracks down to a single track, the resulting single track always has a lower volume and much duller sound than when I just play the individual tracks together.
 
I have a combination of SoftSynth tracks and audio tracks.  I first bounce the SoftSynth tracks to audio tracks (and mute the midi tracks), so I can add the appropriate mixing treatments to the audio versions and can control automation a little better.  I also have some vocals routed to a vocal bus (which feeds the master bus) and route the kick and snare to a drums bus (which feeds the master bus).
 
To mix down, I do this:
 
1.  Select all the tracks I want to go into the mixdown.  Do I need to select the vocal bus and drum bus also?  I've tried this, but it doesn't seem to change the outcome.
2.  Choose "Bounce to Track"
3.  In the options box, I set a New Track as the Destination
4.  For the Source Category, I choose "Entire Mix".  My Source Buses/Tracks is greyed out, because it's just my audio card.  I also have tried "Main Outputs" as the Source category, and then my Source Buses/Tracks is not greyed out and shows my audio card.  The result seems to be the same.  I also have tried choosing "Bus" as the Source Category, and then selecting the Master in my Source Buses/Tracks.  The result seems to be the same.
5.  I select Stereo as the Channel Format.
6.  I set Dithering to None.  Sometimes I set it to Triangular.   The result seems to be the same.
7.  I select all the options at the bottom, so that it takes into account mute, solo, automation, etc.  
 
All the tracks bounce down to a single track, as expected.  I mute the individual tracks and listen only to the new mixed down track.  But it sounds absolutely terrible.  Nothing like what it sounded like when all the individual tracks were playing.  I lose about 3db, and it is dull and lifeless.  Bass is muddy and overrepresented.  Absolutely no top end...can barely hear high hats, etc.
 
What am I doing wrong?  
 

In my projects, I always have or create a Master bus, where EVERYTHING goes out to the speakers. Then when I'm exporting, I like to set it on "What you hear" and have it set to export from that Master bus.

This may not be the "pro" way of doing it, idk...and I'm sure some folks more experienced with exporting can chime in with a more standard solution, but from what I've found (multiple years using these settings), this method ALWAYS, 100% of the time mixes down an audio file that is exactly like what I'm hearing in the project pre-mixdown.
 
Not sure it exactly solves your problem, but it solved any issues for me involving mixdowns where stuff isn't coming out EXACTLY as it sounded pre-mixdown.

In my projects, I always have or create a Master bus, where EVERYTHING goes out to the speakers. Then when I'm exporting, I like to set it on "What you hear" and have it set to export from that Master bus.

This may not be the "pro" way of doing it, idk...and I'm sure some folks more experienced with exporting can chime in with a more standard solution, but from what I've found (multiple years using these settings), this method ALWAYS, 100% of the time mixes down an audio file that is exactly like what I'm hearing in the project pre-mixdown.
 
Not sure it exactly solves your problem, but it solved any issues for me involving mixdowns where stuff isn't coming out EXACTLY as it sounded pre-mixdown.

I'm not 100% sure I got your workflow description right. You are using the "standard" way of routing, are you?: Every instrument and bus is routed to Master Bus? Also Master Bus should be the source for bouncing instead of Entire Mix. This is the easiest way to make sure everything is in your control, and no signal finds pig holes.
 
Your description of the resulting sound makes me think of phasing problems and things due to arrangement.
In the project, do you have, for example, a synth track with bass material plus a normal bass guitar? Or similar sorts of high frequency sounds (like many acoustic guitars)? Or a two hand piano part, including low sounds, and an e-bass? These may offend each other, cumulate disturbingly or cause phasing issues (opposing phases eliminate each other resulting either full silence or defective sound).
Or do you have single source (mono) instruments tracked or copied on two tracks to widen the sound? Or a mono effect on a stereo track which sums all to mono and causes phasing?
 
Or does the bounced track get double-effected: There are FX on master bus that end up on the bounced track.
Then you audition the bounced track through Master where the FX are still on? 
 
Chances are very many, but I'm somewhat convinced the answer lies in the direction of routing/summing, phasing, arrangement.

That certainly does have all the earmarks of a phase issue. I'd suggest starting with an experiment: bypass ALL effects and repeat your bounce procedure. Does the bounced track still sound different from the normal mix?