Deposit to joint account Steve & Mary Smith. Mary is the one making the deposit. Both Steve & Mary are listed in Part I Section A (one on page 1 and the other on page 2). If we mark "conducted on own behalf" does it make a difference if Steve or Mary is the one listed on page 1, section A? In other words if only one account owner is present does it absolutely have to be their info on page 1 or can the absent owner be on page 1 and the present owner on page 2?

I would show Mary on page 1, Section A and check conducted on own behalf, making it clear that she was the conductor. Steve goes on page 2.

Technically, it doesn't matter who is on the first page and who is on second page as long as both are shown as individuals on whose behalf a transaction was conducted and [x] conducted on own behalf is marked.

If there is any FinCEN guidance to the contrary, I haven't seen it.

Or, if you are an efiler, you can use the new CTR and mark each person accordingly on their own page (ie Mary conducted on own behalf, Steve person on whose behalf transaction was conducted).

Our system handles it this way. Deposit over $10,000 to a joint account Steve & Mary Smith. The system automatically pulls Steve & Mary over to the benefactor screen due to the account number being a joint account. In the transactor section if the teller marks "conducted on own behalf" then the system automatically puts the first person listed on the account in that section (Steve, in this case). We are having the tellers make sure that if this is not the person at the bank then they make changes so that the actual transactor will be on page 1. We just wondered if some were not changed if it was a violation to have the person that actually did the transaction be listed as a benefactor on page 2 and page 1 showing conducted on own behalf.

The impact on accuracy is minimal, but if it's the only thing an examiner can find...

Since you appear to be willing to take the extra step, there is no harm in calling the Helpline and making certain it is necessary. (I would not say it was what I was doing, but would simply ask if it was necessary.)

If you were not willing to make the adjustment, then I would refer you to Dani's observation that the issue goes away on the BSA - CTR and suggest you roll the dice a bit until you switch to the new form.