Unfortunately, it looks like your solution has solved the case on one of my projects but not the other. When I try to export the MIDI, the first 11 and a bit bars are cut off when I reimport the MIDI to the session and it changes the project tempo from 120 to 130 and messes with the transposition section as shown in the images.
I have 2 bass midi regions I'm trying to export, in the case of the second one random notes seem to be getting added in as shown in the picture. Any further ideas? I have the project beginning at bar 1 as suggested. (The original, exported MIDI are the purple regions and the MIDI I've reimported into my project are the green regions).