I’ve encountered the same exact thing. When I step through my initial 23.98 AE output in Quicktime, there are no duplicate frames, and it plays back smoothly. But when I re-import the output back into AE and drop it on the Comp icon, I get duplicate frames as I step through the timeline. After I re-output it, the duplicate frames are still there when I playback with Quicktime.
Did anyone find a solution to this?