EA created a different release (1.612) for the download version of the game. Therefore the game is not compatible with the old 1.61b servers (you can only play on 1.612 servers). But apart from that both versions seem to be very similar (no additional patches included etc.). The only major difference that I recognized is that there are currently no IDs assigned to the players ingame (Hashkey, User ID) which makes it impossible to ban a player and not only a nick.