On certain skulls, you need to complete the mission from the beginning. If you miss your jump, or fail in any other way, the skull will disappear, and you will need to restart the mission..not just from the last save point.
Silver skulls do not unlock achievements, but gold skulls will. If you collect all gold skulls and silver skulls, you will unlock the Hiyabusa helmet for your spartan.
I have 2 more skulls left to get, so I'm in the same boat as you.
Also, if you claimed the skulls once before, they won't show up the second time you play it.
I don't think campaign scoring has to be on to get them. Just play the campaign on Normal, Heroic or Legendary.
Good luck!