What the other dude said was right, and the more I think about it I don't think this is even relevant as early as that skull is into the level, but make sure you're actually starting from the beginning and not a rally point. Skulls won't appear if you don't go from the beginning. I also destroyed the anti-air Wraith before getting the skull and it worked just fine for me, just make sure to leave the one by the next part of the level alone.
Like I said, doubt it's relevant but it's another thought.