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I don't think that what you're seeing is the bottom of the image at the top of the page. Rather it appears to be the top of the previous image.
Check your page refresh setting. It may not be redrawing on every page (which is actually OK).
The real question is why the current page is rendering lower than the previous page and why your current image is being cut off at the bottom. It seems like a specific display area, like a viewbox, has been set and the image alignment (or margins, etc...) has pushed it down out of this area.
Since you're using Calibre for the conversion, try asking in the Calibre forum.
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