B.J.
I put bug spray around the base/back of my counters and where the backsplash meets the bottoms of the cabinets at night. (Yes, this is a high maintenance thing to do because in the morning, you must thoroughly wash these areas) I then put bowls of vinegar by the drain in each kitchen sink. I did this every night until I didn't have the flies anymore.
It is also of absolute importance that no fruits be left out on the countertops.