Well, I've never heard anyone use it in Italy. Are you sure it wasn't "grazie DI tutto" or, "grazie PER tutto"??? in that case it makes sense, because the waiter is thanking your friend FOR everything, maybe he gave him a good tip and was also very friendly, so therefore he is thanking him for more than one thing.
The only other thing I can think of is that the sentence is not complete, maybe it was "grazie con tutto il cuore", but apart fom being veeeeeeery cheesy, it also sounds a bit over the top, and would mean "thank you with all my heart". a bit too much for good tip, innit?
cheeres
