What aperture were you at?
I have never experienced flickering from the aperture as is settles in place, although I can see why this would happen. I don't think I have ever experienced this is because my camera, the D3100, being entry level (and becoming a little under-featured for me) has a slow burst rate of 3 frames per second. Since the entire mechanism is considerably slow this would allow some time for the aperture blades to settle before the sensor gets exposed.
If your camera has a quiet mode, I suggest that you try taking time lapses with that and see if the flickering improves. This may include a delay between closing the aperture and opining the shutter.
Did security check the device?