After running Skyrim for about 30 mins or so straight, I start to get these occasional small blue squares that quickly flash on the screen, usually in a corner of the screen. I have an HD 7870 OC edition. My GPU isn't overheating, as it typically hovers around 70 degrees C under load. I also ran DxDiag and it says no problems detected. I'm worried this may be a GPU issue anyway though, anyone know what this means?
More aboutblue flashes screen
Do you have an application running that is trying to steal focus? I.e. applications that try to run on the top of all other running applications.
I do run MSI Afterburner's On-Screen Display Server which I just use to cap my FPS at 60 since Skyrim's V-Sync is terrible. Could this be the cause?