The only thing that comes to mind is not SW release related (at least not 1.03 vs. 2.0b3 - the bahaviour was different in some early pre-release betas): if you play a playlist unshuffled, the tune counter will simply count all tune appearances in child playlists; if the list is shuffled, it will count only unique tunes.

Update: I just noticed that you say you played randomly in both cases... Hmm, I don't know what that could be. Just a thought: do you by 'random' mean root playlist marked as 'always randomize' or shuffle mode switched on?