I got in touch with the abcusers list to try and resolve this problem and got a good answer from them the other day.

According to Phil Taylor: "...you are up against the problem which besets all midi to music converters, which is that the original MIDI file was recorded directly by a human being playing a keyboard, and the timings are all a bit irregular. This means that you have some odd note timings which do not translate directly into staff notation unless you decompose them into smaller notes which are tied together....

This is similar to the problem of playing Irish tunes from written music. You have to be familiar with the tradition to pull it off. In the MIDI conversion problem the situation is reversed. The program is taking a live performance and trying to crunch it to technical rules of music notation.

radriano