It probably is rounding down. How the scenes in FFX-2 work is that each scene gives you parts of a point. Very few parts of the game give you more than 1% at any point of dialogue or full scene, with the exception of certain areas, that DO give more than .20% per line. Fortunately, most of those scenes are skipped by uising the Square function.

Otherwise, you accidentally pressed "X" during a scene that provides you with percentage, and you lost the percentage that you skipped (you can't get it back). Don't worry, there's an extra 4% in the game, total. Percents are given in intervals/multiples of .20%. Not only that, there's the handy dandy New Game+ accomodation, allowing you to get that other % you need.