The score is calculated as the sum of the best scores you have played for each part in a song. You can check your score on the song summary screen.
As an example, a score of 93,650 was received for the most recent play of the song.
The score shown on the Leaderboards (100,100 from the example) is the combined score. It is the sum of the best scores achieved for each part of the song, from all previous plays.
When you re-play the song, the score visible is your best achieved thus far.