One problem you might find (although this may have changed with newer Versions)
If your MIDI files are references in the project, it will play back in in the time signature and bpm that is set in project preferences, not what you have on the timeline. So if you have time signature/ tempo markers, or are using master envelopes, your items might not playback as expected.
(will check later if this is still true - otherwise ignore me.. ha ha)
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