I had a similar issue. I found it was caused by a track's output going directly to the output bus, not my master bus.

JohnRick
Update:
 
Still the same thing. Time to move on to a better software likely. Again, I appreciate input, but this has NOT got something to do with hidden plugs or anything. It's one track only that needs exporting. Fader down to -6dbfs, routed out to masterbus. Main outs are at 0,0, as well as masterbus fader. During playback a very conservative level and not even hitting -9dbfs. Clean track export via masterbus- > reimport the same track=major roofhits.

To be fair, it's not the software otherwise this forum would have been in total meltdown.
 
Try bouncing the clip to itself. This has cured a number of problems in the past
 
If that fails, drag/copy the clip to a new project and try again

What stuck in my eyes was that you route things to Master Bus, but select Tracks as the source. Why not Master?
I don't know if it matters, though.

I have had a really strange issue too with distortion, in my last two songs (and none before). It's a bass drum track in those songs (recorded with a mic), either exported with the entire song or as a single track, it sounds fine on the DAW computer and another comp I tried it on but as soon as I play one of those tracks on my own comp it distorts heavily. I have tried exporting other songs I have done recently to compare and none of them do this but these two. I have tried exporting them in various formats from totally unprocessed to drum replacer and compression at 44.1/16, 48/24, 44.1/32 etc.,  nothing works! I've never seen (or heard) anything like this! Using Platinum with latest updates. *baffled*

JohnRick
 
  During export I choose "tracks", and then "raw tracks". 

Are you using RAW as the export format? If so that may not mean what you think. It is sort of a formatless audio format. The format should probably be wave, unless your collaborator is using some weird application.

Hey all, I found a solution, I EQed those tracks with highpass at around 40 Hz now and the distortion is gone. I guess my main comp couldn't really handle those really low freqs. Thanks for reading! 
 

What kind of limiter do you have on the master bus? Could it be overloading?

I read so many posts like this one, with nary a mention of what happened before the
track stage at gain, so thank you for stating where yours was set.
 
That may be your issue. Try lowering the gain to the level you set your tracks to
instead of adjusting from the track. That will give you more headroom.
 
If the signal is clipping on input(gain pot) it will clip on export If you're exporting to raw,
or even wav if you check the option to defeat Sonar's processing.
(I.E. you will get the full volume of the input no matter what your track settings are.)
Have you checked for this?
 
Mel