Is this because there are no more blocks that need that color? For example, if the gradient you are working on is black (0, 0, 0) to red (255, 0, 0) then you will never need green or blue. They will still fill up once, but not restart because there are no blocks that need its color. Does that make sense?
Something similar happened to me a couple times. The color bar would stop moving with a chunk of black left on the bar. Hitting the manual tick button or upgrading the auto speed got it unstuck. It seemed to happen when the auto speed was at or above 128, and got more frequent the larger the pixel field became.
