Is it possible that the flies are entering the house through the cold air returns and/or the heating/air conditioning vents?? We have a crawlspace for the basement and have determined that's where Chipmunks live. If the flies can enter through our vents, I plan to screen the backsides of those vents. I have found no other source of possible entry into our house.
We bought a house on a golf course in Colorado. After we moved in we found out we had plenty of flies, EVERY single day. The house is big but new (2003). WE asked pest control, they couldn't figure it out. Everyone around here was saying it's a problem with big homes!! In the meantime, my husband wanted to organize the garage so he hired a handyman to hang ladders and stuff on the wall of the garage. The handyman started drilling holes in the wall under a window but he couldn't find the studs. He pulled the wall and found that under that window (there is a porch above that window) all the wood was rotten but not wet. It turned out that there had been a leak on that porch and previous owners had replaced the porch, however, there were no signs of the water getting inside the walls, hence the rotten wood! So, we had the contractors replace the entire wall. Since then we have had no flies. Flies were getting in through that rotten wall. If my husband hadn't decided to rearrange the garage, we would have never gotten rid of those flies. I am not sure if this will help anyone but it sure is a strange way of finding out how flies get into a house.
I would be interested in your answer to Dano0430's comment.
You could be seeing "Drain" or "Sewer" flies, particularly if you find these in or near your bathroom or shower. They are small black flies, that are weak fliers and harmless, nothing like the typical housefly. They come up in the spring with the change of temperatures. You can put a piece of tape over half a drain and see any are caught in the adhesive.
I typically use two treatments; "Foaming Pipe Snake" drain cleaner to coat the trap pipes, and follow up with a build-up remover in each drain in the house. The idea is to remove/reduce any organic slime buildup in your drain pipes.