How many times have you sped it up? ie, how many frames per second.
I know the last time I shot a time lapse - I used a lens without an aperture ring, which means each time the camera opens up the aperture, the aperture is physically slightly different each time,leading to a variation in exposure that isn't noticeable in photos, but is very obvious in time lapses.
But in your case it is a bit more pronounced.
What software did you use? Perhaps the software automatically inserted a black frame in between each photo resulting in the consistent flickering? Try Windows Live Movie Maker to make the same timelapse and see if it makes a difference because WLMM is free and you can quickly see if it is a software problem