If someone comes in to the bank to cash a check made payable to him and drawn on our bank what boxes do we check in Part III. Is it ok to check the box for Negotiabe Instrument(s) cashed? What about the Deposit/Withdrawal box? Thanks for your help.

Negotiable Instrument Cashed.
Withdrawal is only used when the beneficiary is also the account owner.

I concur.

What if a member brings 25K in cash. Deposits it to the checking account and then has a cashier's check cut to their title company for their closing.The 25k was deposited first because our system wouldn't allow the cashier's check to be cut otherwise. We would complete the CTR for 25K cash-in AND 25K cash-out?

Remember the rule - cash in hand must pass through the bank's doors to be reported. So report it as a 25K cash in/deposit to the customer's account. But the purchase of a cashier/official check is not a cash out transaction - they did not carry 25k in cash out the door. Had your systme not required the deposit, it would have been a 25k cash purchase of a negotiable instrument. Remember that the CTR must reflect how you can research the details later for law enforcement should they ask about the transaction. If you listed this transaction as a negotiable instrument purchased for cash, it would not reflect your bank records which are a 25k cash deposit & subsequent account withdrawal to purchase the official check.

I somewhat agree...

We've been told that in this scenario you would check negtiable instrument cashed AND you would check account number and list the account number.

Auditor from McGladry said that if the account was housed at our bank, the account number was affected and had to be listed

I don't disagree. No one asked about marking the account number box, so we didn't discuss it.

It clearly says, "drawn on our bank"....therefore you would list the account number