Allowances are due if you are on-station during the meal window; it has nothing to do with when you arrive at or depart the hotel.
Another station to watch is Accra; I was short changed there on one occasion but had left the reception when I discovered the error. The following time the allowance was similarly 'discounted' but I brought it to their attention at the time and was paid the difference.
Suggest always check what allowance should be off briefing sheets and count it before leaving reception.