Al-Khwarizmi is right, the rests are not there - yet. The rests are very tricky (see other comment) to get exactly right. I've figured out most of the note timings to be precise enough to render the score accurately but the rests do not have any representation in a midi file, so you have to make them up as you go.

There are other problems like that, such as trills and other ornamentation, which show like a bunch of note on/off pairs in a midi file but as a single note with a decorator in the score. Reversing those is non-trivial, as are grace notes.