There is definitely something deeper going on here, and it has to do with the changing tempo of the song and not the drum breaks, as I had thought. I have opened a support ticket ticket #(84325).
If you can e-mail me, I’ll send you the audio track and the MIDI Tempo file to upload into tracker.
When I uploaded the tempo file, it got me closer. But the tempo changes don’t seem to apply when I drop the MIDI file into the DAW.
I did check the audio file is not already cut off.