IMO, if the customer deposited the funds then immediately withdrew them to purchase the check....they intended to purchase the check with those funds.The customer may think its bank policy to deposit first, or they wanted to for their own bookkeeping.
If the cash deposit happened yesterday or two days ago, maybe their intent was to offer a personal check and the person wouldn't accept a personal check.....I would definitely ask the questions to find out. For a deposit from last week or a month ago.....again, just my opinion, I feel the funds were on deposit and not immediately withdrawn to purchase the check and wouldn't complete an MIL. Again, these are just my opinions and how I would advise my bank in those situations.
I think if you have a definitive answer when asked by the regulators and follow FFIEC guidance and your procedures you'll be fine.