[Daniel McKleinfeld] “The After Effects project is based on the HDTV 1080 29.27 preset, with the pixel aspect ratio set to Square and the frame rate at 29.97 (non-drop display).
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Rather than use a preset, drag the ProRes footage onto the New Composition icon at the bottom of the Project Panel.
This will make a composition that conforms to the footage dimensions and frame rate.
The only other thing I can think of is that the footage is 1080i not 1080p and the footage is not interpreted correctly.