After more consideration to the message QI172W - it appears the Copyauth job is working as designed. The product is designed to grant execution per level or tier.
Primary ID one granted several ID's Execution on certain plans and that worked, but it also granted another ID Grant Authority. So primary ID is the first tier, and the other ID is the 2nd Tier and it granted several IDs execution on certain plans, these were the ID's missing from the initial execution of the Copyauth job. By re-submiting the Copyauth job again you'll see the grant execution on the plans for the 2nd tier.