I looked at the entire flight history again and realized what was happening. My VIE-FCO flight was booked on Alitalia in Y. Delta's trainwreck of IT system saw a full fare economy flight for a medallion PAX and "upgraded" it to F - which would be first class, except first class doesn't exist on that flight at all (only business, J). "F" class isn't eligible for mileage accrual on Alitalia because it simply does not exist.

Another call to the Skymiles line and they saw their mistake and apologized for the "glitch" (as they called it) and confirmed they were able to see that the flight was booked and flown in Y and that Y is eligible for milage accrual.