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Remove de DOCTYPE line. That DOCTYPE is for XHTML-only content, and you are including an <svg>, which belongs to a different type, that's why the W3C validator fails (it's not valid XHTML, as declared by its DOCTYPE)
Epubcheck accepts it as valid because (I believe) ePub explicitly allows documents including both XHTML and SVG content.
The DOCTYPE line is optional, but if it's present, it must be correct. The one you have is not, so it should be removed, and I think epubcheck should give it as an error too.
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