Taken from the achievement guide:
To get the "Hidden Treasures" and "Bag Them Bones" achievements, each level has to be done in full for either the secret or normal skulls in one try. Meaning you can do the level once and get all normal skulls, then do it again to get all secret skulls - but each type must be done in one attempt. You can't get skulls 1-5 in one run, then 6-10 in another. All 10 must be shot in one go.