Multitrack Mixdown Sounds Different After Export

There have been a number of posts about this issue, but I have yet to see an explanation, let alone a solution. Basically, upon exporting a multitrack session, the end result sounds different than it did in Audition. Moreover, the waveform comes out looking different between the two.

Here is a side-by-side comparison.

The top waveform is what Audition created. The bottom waveform was captured by playing the session (in Audition) and capturing it with Soundflower.

The session itself comprises five tracks, four of which have automatic pitch-correction applied to them. The mix has a parametic equalizer, dynamics processing, and studio reverb applied to it. All of these effects come through just fine, but as mentioned, the end result is different than what Audition plays back on its own. The incongruity is particularly noticable in a sudden jump in volume at the very end.

I'd love to know why this happens and how it can be fixed.