Welp, after troubleshooting for quite a while, including finding the first version edit I had that worked properly, and manually rearranging events to match that file and still not getting positive results, I ran mod2 (working) and mod3 ("not working") through Sema's test_midi_files, and compared the results with Notepad++ Compare plugin.
Literally the only difference between the two files was the cymbal that was being played. In the "working" one, it was "China Crash". In the "not working" one, it was "Splash". Doh.
So it HAS been working this whole time, just the instrument was different, and thus the pitch shifted sound would also be different.
To verify, I changed the pitch bend range from 12 to 36, and it was 100% applying the pitch bend.