ctrl+F
zooms the camera to 100% and pans the camera so the skeleton is centered. If you press it, play an animation and press it again, zoom won't change but pan might, to center the skeleton.
If you are pressing ctrl+shift+F
that zooms the camera so the skeleton takes up the whole screen and pans the camera so the skeleton is centered. If you press it, play an animation and press it again, both zoom and pan might change.
You don't appear to be pressing ctrl+F
because your zoom level is not 100%. Your screenshot shows you are zoomed in all the way:
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100% would look like this (the ball is lower):
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Can you show two screenshots of your skeleton in Spine on frame 0 where the skeleton looks different in each screenshot? Please include the dopesheet in the screenshots.