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There is an Amazon-supplied program called Kindle Previewer, which included the Kindlegen routines - the "official" way to convert epub to Kindle formats. The plugin for Sigil merely calls Kindlegen, which will have to be already installed on your computer.
The conversion in Calibre can be rather more helpful. For instance, text-indent:0 is ignored in Kindle, you have to instead set a very small positive value. Calibre sorts this out automatically. And although Kindle tolerates a cover image in a svg wrapper, subsequent svg instances will break the Kindle version. Calibre also corrects this.
So convert in Calibre. The author anticipated many pitfalls in epub>Kindle conversion. Take advantage!
Let's see your epub code, Arran. I think the problem will lie there.
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