Luke,
I produced an epub with your tool, and it worked fine (as usual

).
Only remarkable that margins left and right turned out very narrow to the edge of the screen. @page settings showed:
When I tried to split margin settings in
Code:
{
margin-top: 5pt;
margin-bottom: 5pt;
margin-left: 7pt;
margin-right: 7pt;
}
at least the last mentioned settings were ignored; margins remained narrow.
I can't see that margin values are affected by other css-settings. Does your tool touch the page-template.xpgt in the OEBPS?
I should mention that I make an epub-to-epub-conversion with calibre afterwards. It's quite possible that this has some impact, although at the page-upset margins are put to 5pt at top and bottom, and to 7pt left and right.
Not really a problem, for I can change margins on the device itself, but just out of curiosity ...