Make sure you are using fresh Hydrogen Peroxide. It has a tendency to weaken as it sits around. Exposure to sunlight also weakens the solution. That's why its sold in an opaque bottle.
Another reason is that there is still some fat residue in the skull. Some skulls just need to be boiled a little longer with the 3S Degreaser. Out of the hundreds of skulls we've done there have been a few that needed to be boiled for another 15 minutes after they were bleached. When pulled from the water they are all done. You don't need to reapply the bleaching paste. Just put it into boil with the 3S Degreaser solution for about 15 minutes.