I doubt it has to do with the custom synching - if you see the note on the highway, you play it when it crosses the string. If it is off on how it is displayed (not synched to the song) you just need to play it as it is shown. It could be that it is slightly off and you are playing how the song is supposed to be played (and how you hear it) instead of how it is displayed.If you like the song, don't worry about scoring or seeing the late, miss alerts on screen. Let the creator of the custom know though - there could be others having the same problem and it very well could be a charting issue or a note highway speed issue that could be fixed.