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I have two clips, both shot with the same settings but one clip has a higher height of clipping on the top and bottom of the clip. What's the reason for this?
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More movements in the clip.
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Warp analyses each clip, in the attempt to get a satisfactory level of stabilization with the least cropping of the image. So as Ann notes, each clip will have a different "zoom" amount, and may be slightly shifted on the X/Y axis.
So when stablizing, at times you need to apply a bit of zoom or positioning changes to the beginning of the clip before/after if they need to match.
Neil