I don't think that contradicts it neccessarily, its not a temporary increase that you're trying to apply. Your DM could rule that the new skill points wouldnt come until next level, but I don't think this would fall under that category at all. Its the difference between quaffing a potion, and choosing one of your 4 extra ability points for your character. One is incredibly munchkiny, and the other is built into the game. Its clear that rule was written to prevent the potion scenario, not the skill point increase. Just like when you get a con point at level 4, you get the hit point increase immediately.
Just my two cents.