Answer:
Was there a
* deposit,
* withdrawal,
* exchange, or
* other payment or transfer
of more than $10,000 in cash?
Since your bank had already removed the cash from the box and had it in your control, my opinion is a reportable "transfer" took place when you gave it to the spouse. If a co-worker wanted to debate the point my response would be: "Filing it is less time consuming than talking about it, we are filing it and going on to what's next."
The fact that it did not show up on your system is a partial explanation for why it was not filed in a timely fashion, not an excuse for not filing it at all. Write a brief memo to file explaining the oversight.