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It does not depend on Scrivener itself, but more how the blank line is coded into the ePUB. That can be done in various ways. The purists will insist you use margins to create a blank line and although they are correct, your reading program need to honor the stylesheet in order to represent it (btw, a reading program that does not honor stylesheets is a broken program in my book...). Another much used method is the empty paragraph. However, a lot of readers and reading programs will discard real empty paragraphs or paragraphs with only a space inside it (e.g. <br /> or <p> </p>. That is why you need to enter a special space inside it to work in all cases: <p> </p>.
So, perhaps Scrivener has an output option for this, otherwise you need to check how it is put in the code and correct it there.
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