The flicker comes from the camera's light meter not being perfect. So if you're in Aperture Priority mode and shooting during sunset you'd like to see the shutter speed to do this on successive shots as the sun went down:
1/60, 1/50, 1/40, 1/30
Ideally the shutter speed would linearly decrease, creating a smooth transition from light to dark when played back as part of a video.
However, what it usually does is this:
1/60, 1/50, 1/50, 1/60, 1/50, 1/40, 1/50, etc
So the variation in shutter speed causes the flicker when you play it back as part of a video.
You can use Manual Mode which solves the problem. However, if the light is changing (sunrise/sunset) this doesn't really work. The Manual settings that are correct for 30 minutes before sunset aren't correct for when the sun's on the horizon. It'll be well exposed 30 minutes prior to sunset, but really underexposed at sunset. You can try changing the manual settings, but this introduces other problems like moving the camera slightly (making for shaky video) or jumps in the video because it took you a minute to change the settings.
One solution is to use software that compensates for it. We (Digital Anarchy) make one called Flicker Free, but if you google 'time lapse flicker software' there are others.