This can happen if the original icon was smaller than 128 pixels high. When an icon is added, calibre scales it down to 128x128 pixels preserving aspect ratio, but does not scale it up. The graphics toolkit will upscale a single image if needed when it is used as an icon, but when images are combined into a composed icon this upscaling does not happen.
Solution: ensure that all your original icons have at least one dimension greater than or equal to 128 pixels. Best is if they are square with both dimensions greater than or equal to 128 pixels.
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