swamptooth
i cannot reproduce the in-project bounce. it would be nice to know the settings that were used to be able to recreate it.
one really odd thing is that the waveform i see in track 44 is empty (silent) until bar 17:04 even though there is audio.
I think most of the inability to null is due to FX not reproducing the same output every time. My own bounces won't null with the live guitar and vocal tracks, which is common when individual tracks/buses aren't frozen/bounced before doing the master bounce. But there may also have been changes to the project after that bounce.
One odd thing I found was that track 16 (acoustic guitar doubling, panned right) appeared to be audible, but was silent when soloed. Turns out both lanes are muted, but the comp track clip appears active (not grayed out). I guess they decided the mix didn't need it, but it was odd to mute the lanes rather than the track. I think the Comp track should reflect when all underlying lanes are muted like this.
I'm not seeing the flatline to measure 17 that you are.