Having written MIDI import software, I can tell you that the main problem is that MIDI does not understand notation, it just deals with Note-on and Note-off commands. If the music is captured from a performance, then these will NOT be precisely matching the specified lengths, and indeed you don't want it to, as it would sound too robotic. There can be up to 384 MIDI 'ticks' to a quarter note.
Try Quantising the MIDI file before converting it (You need a sequencer for that)

(Actually, the fault is with music notation, which is quantised, not MIDI)