OK - I have been doing this a fair amount of time/years now and recently mixed one of my four bands EP's to their full satisfaction.
 
Must be a bug of sorts. I am exporting clean (raw) tracks for one other person. Let's say I'm going with saxophone.
Gain 0. Lowering fader to -6dBfs and signal is well below -12 at this point. All FX are off, and it is only routed to a master bus, that is going to main out. Master Bus has a safety limiter on at -03dBfs. During export I choose "tracks", and then "raw tracks". Looking/hearing back at the waveform it is still distorting. So I try to lower every fader possible. Still distorting. So I choose export via main out - same thing. Entire mix - same thing. No automation read, no fx, nothing. Just clean tracks, but the signal during playback is going at a very modest level to the mains. Then after export - massive distortion, which is also the case when reimporting the track to look at it. Never happened before. 
 
Input? Going Samplitude or DP?

Hi.Could it be a mismatch of sample rates (between project and samples)? 
What audio interface do you have? Do you have the latest drivers for it?
Best of luck.

No mismatch. Always record 24/44.1. RME UCX is my AI of choice. Always the latest drivers, but that is not an issue either way since it's the exported file in itself that get's hot even if all gain knobs/faders and buses are close to the floor. I just tried muting the track I'm going to export, and then exported. File ended up having a massive amount of white noise on it.

Check you routing again. Look for sends or tracks that are not routed as you think. 

John
Check you routing again. Look for sends or tracks that are not routed as you think. 

Again - all that has been done. Have worked the past five years, and now suddenly does not.
Clean track->master bus->stereo out. No sends, and I only export that single track.

I know a few versions ago your Pan Law settings set at 0 would cause some overages.Also check your interleave settings so you are not summing incorrectly.This was an issue not too long ago. Just spit balling..

I had an issue, not with Sonar in particular but with RME Totalmix.
 
All outs were also routed to analog 1+2 out - so running headphones out on one and then on main - became 6dB extra which distorted.
 
So I removed that extra routing to 1+2 in Matrix view - and that fixed it.
 
Don't know if applicable in your case - do you run a headphone mix too or something?
 
A bit puzzled over description - you say actual signal is below -12dB, but you had to set a limiter on -3dB:
a) why do you need that if so low on everything?
b) does limiter say any limiting done?
 
Either way, I would look at Totalmix meters what is moving with a playthrough.
 
No luck, look through dc offset and remove that.
 
Still no luck - did you have offset mode for fader on at some time - meaning there might be an internal offset done to the automation your don't think you have, because it's a straight line. Check the level on it!
 
Meters set to peak, and not rms?
 
Now, I'm out of ideas....

got a compressor somewhere trying to make itself known?

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.

If you like you can make a mini project of this.
 
Select the track and master, and save as track template.
Start a new blank project, insert this saved track template.
 
And we can run it from here and see - if you want - or don't.