I'm sure I've seen many posts confused about what they've exported from Sonar and how it differs to the original track, and the usual answers are "are you sure there's no effects on the original which are not being exported" or "is it a synth with some kind of random elements in it." However none of these answers have ever assured me that what Sonar exports from a synth is 100% accurate as expected. I frequently do a check with one track's phase flipped and I rarely get full cancellation, in fact frequently there is a ton of information left over. And when I play the original back with the exported wav, I usually hear some kind of phasing going on as if the timing is a little off.  And not only that, but the levels are frequently different in places, sometimes as much as 1db. 
 
Case in point, I just exported a synth track, an instance of Waves Element playing a very basic organ sound. There is no modulation going on in the patch and no effects on the track. There is some synth automation being exported with the track - the cutoff filter. But again, I see no reason why that should make any difference. Upon playing the two tracks together, they sound phasey. Flipping polarity on one, all that disappears are the bass frequencies. And comparing peak levels on both tracks, there are many places at which the difference is up to 1dB. 
 
Does anyone else find this sometimes or is it just me? 

I freeze
Never tried a null test with two freezes though.

Since synths are supposedly modeled to be "analog-ish", I expect there to be a bit of variation from one play to the next so that's why I freeze, so I hear the same thing everytime.

Is it possible the export is just shifted by a few samples? What happens if you zoom in and realign, then try your test?

Waves claim Elements models analogue voltage-controlled behaviour. So it's hardly surprising that two passes through the same MIDI result in two different results. If they nulled perfectly that would demonstrate that the kind of continual small (sometimes not so small) variations that are normal in analogue CV synths are absent and therefore that Elements ignores a big part of why analogue synths sound the way they do.

You are getting too technical about it and overthinking it.  The big question is simply how does the bounce sound? Try switching A/B back and forth between the original VST and the bounce. Does it sound the same? If it does, move on.
 
Stop using your eyes as well.

Create a second track with the same synth, same patch, and same MIDI data. Match levels and flip the phase on one of them. Don't export, hit play and see if the synths remain canceled as they play or not.
 
Bear in mind that even a simple organ patch is likely going to have variations, especially if the manufacturer wants to make it more "analog" by emulating drift.
 

Jeff Evans
You are getting too technical about it and overthinking it.  The big question is simply how does the bounce sound? Try switching A/B back and forth between the original VST and the bounce. Does it sound the same? If it does, move on.

Missed this before writing my reply, but...excellent advice that applies to more than just this instance.

To be honest it's not entirely the lack of complete phase cancellation that makes me think - it's more the phasey sound associated with two tracks being a little out of time with each other, and I can see that they are a little shifted from looking at the waveform. I also get worried by the difference in levels, sure you'd expect maybe a fraction of a db's difference if it were the tolerances involved in analog component modeling, but for instance on this track the exported version kicks in with a peak that's a full db higher than the original track. That sort of stuff I wouldn't expect, unless there was some random modulation going on. I will do some testing in a fresh project. 

I have come from an era right back in the analog tape multi track days where I was producing a lot of synthesiser music and printing audio from midi parts etc and the tape playback was never as good as the synth playing in real life yet somehow it was not such a big deal. I think today I can honestly say we have got some amazing quality now in this area and really transferring  either external synth parts to audio or rendering internal synths has really never been better.
 
What Craig is saying is true in terms of synths having lots of internal modulations going on even if they are subtle so every time you render you are going to get very slight variations. The only time you may get close to prefect nulls etc is with sounds that are very static and have no movement whatsoever programmed into them and they are usually very few.  We tend to not like those types of sounds.  But in some situations they can actually work better.
 
The level variations may be coming from the fact that when you try to null things out because LFO's are in varying parts of their cycles and are not synchronised anywhere, that is where there may be some slight cancellations going on.
 
I do agree though that some synths e.g. Omnisphere (there was a bug for a while with fast bounces etc) may prefer real time renders because fast bounces can play havoc with some the more very deep and complex instruments with huge effects processing going on etc...