Company A and Company B are separate businesses, have separate EINs and separate names. They each have multiple owners, with one owner in common. They each deposit cash, then ACH funds out to the main holding company. The only transactions in their accounts are cash deposits and the ACH debits out, so there is no comingling of funds between the businesses. (FYI the cash in/ACH out is consistent with the industry they are in.) It does appear that both businesses ACH out to the same entity. Each business has its own manager who makes the cash deposits, so there is not a common conductor. Places of business are separate, although their holding company has its own separate address. The businesses do not seem to share employees. For CTR purposes, would the fact that the outgoing ACH transactions from both businesses seem to go to the same place be considered comingling of funds by Fincen, and that cash deposits from both businesses would be aggregated together? I'm thinking no, but I've been overthinking it, so now I don't know what I think.

Based on your explanation, I agree with you. Payments to the holding company that are reasonable for each business don't suggest comingling of funds to me.

You have clearly laid out all the reasons not to consider this a case of commingling of funds, Trust your instincts and stop overthinking and second-guessing.

And, by the way, the word is commingling (double "m").