I have now updated all the monsters on the D&D 3.5 and Pathfinder NPC Generators to correctly store skills as skill ranks and a separate racial bonus. Before the change the racial skill bonus was stored as extra skill ranks, this meant you could not allocate more points to them greater than the HD in pathfinder or HD +3 for D&D 3.5.
I have tried to match the skills to the monster manual there were a few monsters that did not work out correctly. These I have tried to allocate the correct number of skills ranks, this has sometimes meant adding extra skills (if the monster had not used enough skill ranks) or taking off skill points or adding an extra race bonus to make the figures match.