Screen capture doesn't cause the screen to flicker or change in anyway, unless what ever is doing it was badly written.
Otherwise it might just be a refresh problem. I know on some monitors the refresh is at 60 hertz, such as on my monitor here at home. And at times the screen would blank out for just a sec and then come back on and it would happen at very random times. Turns out I just had to drop the refresh down to 59 hertz and the problem was fixed.
For now my monitor is back at 60 hertz and dont have any problems. I have 3 monitors hooked up. When my main monitor had the problem is was when I was using the dvi port on the back. But now since I have 3 monitors I have it using the display port on the back instead and it is fine at 60 hertz. So I am not sure if the problem was the port or the cable.
Shane