I have been working with this problem for as long as I can remember. All I do, is simply copy and paste the midi file and bounce 2 bars (or more...) To audio . That way I find the second bar will start at the begining where it is supposed to. Or like you say, you can also move the audio file once it is bounced. The only problem with this, is that it means you HAVE to bounce to audio when working on a track, or you will have problems in the final mix. I guess most people do anyway nowadays though. I recall it actually says in the manual to give the midi notes a bit extra on the begining.
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