Personally, I've never truly been a fan of multiple (mini) audits throughout the year. I prefer full-blown system audits. It does require a commitment from internal resources for a larger chunk of time (instead of small chunks over a space of time), but I find it provides a much better picture as to the state and health of the management system.
As for the CB requiring makeups, I think it's questionable and unless it's an explicit contractual requirement I might push back. If it is an explicit contractual requirement, you have a contract review problem.
