I don't know that I have an answer for this but I've never seen the problem. I do most of my reading in Moon+.
You mentioned that it might be something in the CSS and I do have Disable CSS Styles turned off in Miscellaneous Settings. I don't really know a lot about CSS or HTML or epub but I have Calibre set to format books the way I like them and that's how I want Moon+ to present them, which is why I turned off CSS. So this might be a clue that you're right that it is something in CSS.
Sorry I can't be more definite but hopefully that might help a bit.
Barry
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