Interesting. The flashing at least seems to be an isolated System Preferences bug, as I don't remember seeing it in any other applications. Would be better to compare a larger number of UI interactions - Finder, Safari, Exposé/Mission Control, iTunes, etc., to more clearly establish a pattern rather than just claiming it anecdotally. Not saying the pattern isn't there, but proving it would be a breath of fresh in air…
It highlights that the buttons are disabled then enabled when the animation has finished.