Frontmost app's Main window loses focus randomly

Sep  1 12:04:52 retina.local WindowServer[91]: CGXSetWindowListAlpha: Invalid window 0
Sep  1 12:04:53 retina.local Dock[35334]: CGSReleaseWindowList: called with 12 invalid window(s)
I keep seeing these in the logs when it happens. It is obnoxious to be in an app and then hear the error noise because the app I am currently working in loses focus for the window I was working with. For example in Mail, I can be working and the window will lose focus so keyboard shortcuts stop working.

I am having the same problem, and here is what I have figured out so far;
I installed a stopwatch application so I can time it, and it is happening exactly every 5 minutes. Moving the mouse, changing the foremost app, activating the screensaver, or anything else I have tried doesn't interrupt the timer. It will still happen exactly every 5 minutes.
I am currently looking in the console logs trying to find anything that is going off every 5 minutes.
It happens even while typing suddenly I will get beeping because the top window I am typing on loses focus. The application name in the menu bar does remain the same as the current application, so another application doesn't seem to be coming forward, just the top window goes inactive.
If anyone else is working on this issue and wants to see if their problem is exactly 5 minutes also, you can install the stopwatch application here; http://www.macupdate.com/app/mac/42353/timi
I will update here is I figure out which application is causing this problem.
The answer shouldn't be "reinstall your OS" for every little problem as Apple always says.
Hopefully we can figure this out without having to resort to such a drastic measure.

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