Maria, my system works the same way, so I will explain. In most banks with an in-house proof department, any posting that is done over the counter is only a 'memo-post' (spaceholder) which is replaced by a final post after proof completes the work. This is the situation the lglover described.
In banks like mine, and the original poster's, we do not have in house proof, so we use a service bureau to clear checks. All checks, on-us and transit, are sent to them. They also receive our inclearing checks. Each night, they send us a file to post which includes inclearing items as well as the stuff we sent them. To summarize- our OTC items clear like inclearing items from other banks. For that reason, I would say the holds make sense, and Reg CC doesn't apply.
But I do want to offer a suggestion to the original poster. Talk to your core processor/service bureau/whoever abotu gettign you the ability to 'kill' the check at time of presentment. We have this option, and it has saved us from getting burned on countless occasions.