Make sure Free For All scoring is turned on, and check the score needed per level. Gold Skulls (if activated) will enhance your score by a set multiplier, Silver Skulls won't. Difficulty rating also miltiplies your score, as does how fast you complete the level.
To turn the scoring on, go to Mission Select and press the X button as party leader to bring up the option to turn on Skulls and scoring modes. If you need help, PM me and I'll go through on Campaign with you.