The Quad Capture uses a GUI mixer. I suspect if you turn down a fader here, or add compression or ?? it might result in a change to your bounces. Worth a shot I say. 
 

If I am bouncing from track to track, would the interface even affect it?

No, you're right, interface mixer settings shouldn't matter to levels inside the project.
 
But we still don't know what your Source selection is for bouncing/exporting, which is a major factor in the result you get. If you bounce a single track to another with Source = Tracks, I wager it will bounce at the expected level. If not, somethings's going on with gains, offset mode,  mono/stereo interleave, mono/stereo track format, pan law or... something. 
 
Assuming a single track bounces at the correct level with Source = Tracks, then you need to look at the bus I/O levels (both software and hardware) that get involved when you use Buses, Main Outs or Entire Mix as the source.
 
Another possibility if it's only synth tracks that are changing level is that the rendering process is producing a different level than the live output. Try freezing synth tracks first, and make sure the levels are not changing at that point.
 

It's certainly worth double checking all of the above, especially the gains at the top of the tracks AND busses, including the master bus.

What happens if you freeze both tracks, copy the results into two new audio tracks routed to Mains, then solo these two new tracks? 
 

Have you checked your fader levels vs monitor volume knob? The file will export according to the settings on Sonar. If your Master fader is set to -6db, for example, but you have a nice volume level because of your hardware, you may find that this is a cause?
 
And, not wishing to teach you to suck eggs, but you have exported "Entire Mix" and made sure all the little boxes have been checked?