gman, You can try running the undupe.cal script against the tracks of your first file to remove the duplicate notes. Actually, the script say it will remove all duplicate events, not just notes.
I have tried undupe.cal from ProAudio9 and from Sonar X1 Studio and got the same results. That is, the duplicate notes were removed except for one pair of notes at time 31:04:107 (M:B:T). I can't see why those don't get processed - they are duplicates. The other duplicates do get processed leaving just one of the duplicates.
So, in ProAudio9, select the track of interest and then use Edit>Run Cal... and navigate to the undupe.cal file. It asks for a window number - I have no clue what that is about but after trying several different values I find that I get the same results with 0 or 1 or 2 or... In my testing 399 duplicates were removed from track 1 - Melody.
If you don't have undupe.cal you can download it from this link:
https://www.dropbox.com/s/5scrakz15jr08yi/UNDUPE.CAL Good luck!