Melodic Intro and/or Ending out of key
Try to reduce the "Key Detection" value in the "Melodic Parts Settings" in the "Part Settings" window.
The Key Detection method will in some cases detect the key wrong.
If the number of measures for key detection is reduced this will most probably reduce the number of active notes and might give a better result.
In files with modulation (key shift) in the "Key Detection" area you will get this problem if the modulation point is within the "Key Detection" measures.
Missing notes in some channels
Try to uncheck "delete non-scale/non-chord (channel) notes" in the affected channels in "Conversion Settings" in the "Convert and Save Settings" window.
This "delete..." option is to avoid notes not belonging to the scale/chord of the key you are playing as these notes could create disharmonies.
Style makers have discussed this topic many times; but the conclusion is not clear. Sometimes you will get better sounding style unchecking this option.
The default setting is kind of conservative setting which might be to "hard" in all situations.
Miss the "melody" voice in non Melodic Style parts
The voices used for "melody" in "Melodic Style Parts" are by default deselected for use in "normal" style parts when a voice is defined as a "Melody channel" in the "Melodic Parts Settings" in the "Part Settings" window.
However you can manually reselect any of these voices in the lower part of the "Part Settings" window AFTER setting parameters in the "Melodic Parts Settings".
Converted style sounds out of tune
The program has an internal chord recognition method for transposing the original MIDI file to comply with the Yamaha style specification.
This method can get confused if channels with primarily "melody line" content are used for this chord recognition.
Therefore if you want to use these channels select "delete in Chord recognition" in "Conversion Settings" in the "Convert and Save Settings" window for these channels.
All/some channel pitches are too low/high
In "Conversion Settings" in the "Convert and Save Settings" window transpose the harmonized (non-melodic) channels individually up or down.
In "Melodic Parts Settings" in the "Part Settings" window transpose the non-melodic channels individually up or down.