Recently, I have this problem too but I don't think it is Sigil causing it. I use:
<div class="scenechange"> </div>
for extra white space between scene changes but the disappears after putting the epub through calibre leaving <div class="scenechange"></div>.
This causes the whitespace in epubs to be smaller than I wanted but they are okay in AZW3 files.
If I increase the top and bottom margins in the scenechange class in the CSS file they display better in epubs but too large in AZW3.