Depends upon what kind of flies they are. Any chance of an image or two?

For cryin' out loud.....how teensy are they? Fungus gnats?

They are tiny little buggers, they are hatching in droves from the seams in the window frames, but they don't stay that way for long. We had a terrible time with flies through July and part of August, I have never seen them so bad. The local McDonalds was shut down for a time because of them.

My wife has been working the area with vinegar, that with cooler weather should take care of them for now but what can we do to keep things under control next year.

Romore, the image isn't helpful. All we can see is a little speck.

If a McDonalds was shut down, perhaps this was newsworthy and the general type of fly was mentioned in a news article.

I'm not sure you can caulk the area you describe, but it can surely be screened for next year.

I would personally use any of the common flying insect sprays; a little of that goes a long way in such a small problem area. Many flies are attracted to the yellow sticky traps. I though vinegar attracted flies--are you trapping them in some manner using vinegar?