In Protools – I:
1) Get my backing tracks working perfectly – including midi (usually just patch changes and a midi click for future use).
2) Once they’re good to go- I click on file->export->midi file
3) I select Type 1 (Multitrack) and save the file.
Once I’m done that, I close the session and RELOAD THE MIDI FILE to check it. (That’s how I’m sure it works). If it’s all good, off to uTool I go.