I downloaded after effects CS4 and my composition settings is 600x400, square pixels, 29.97fps.
I rendered the video with these settings:
well the rendered video keeps on skipping as soon as it hits the first keyframe, it starts to skip throughout the whole video. I tried testing that in cs3 using the exact settings and it played smoothly.
What are you saying by "skipping"? During playback in QT or when re-importing? In both cases you would only see discrete frames which should not flicker/ jump/ skip. Only RAM previews occasionally would, due to the timebase correction and possible mixing of framerates in combination with your screen refresh. If you are within AE, you may wish to check your OpenGL settings. For QT player the results should be identical. The only thing I can think of otherwise, is the frames not being stored correctly in the first place, which usually is a matter of your system choking when using multiprocessing, so turn it off or adjust the settings...