...With Scrobblit, you will not have any problem of this kind, since it will detect all your scrobbling, in particular detects the iTunes song which has the counter (a number that counts the times you've heard the song) increased. And if an error occurs, you can choose of not updating the iTunes (or Rhythmbox) database, so you'll restart the application and detecting again the tracks.
Scrobblit was written in Java, so you must have the JVM on your computer; you can download it here: http://www.java.com/en/download/.