Maggie,
I'm a little fuzzy on the details, but I will say the same thing rlcarey did a bit differently: If the transactions were not eligible for exemption or thought to be eligible for exemption up front, there's not much chance they could be exempted after the fact.
I don't see that you are falling on your sword by filing them late. Banks often find CTRs during audits and investigations that the normal operation of their systems would not have brought to their attention. That's one of the things you mention in the memo rlcarey talked about; i.e. it wasn't a mistake, it was the result of enhanced due diligence over that normally applied to the customer. While I think the proper placement of the memo is in your file, not in the envelope with the CTRs, I won't debate the point. Just keep a copy for your files.
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In this world you must be oh so smart or oh so pleasant. Well, for years I was smart. I recommend pleasant.