Have you tried modifying the <html> tag at the start of each XHTML file to read:
Code:
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:epub="http://www.idpf.org/2007/ops" xmlns:math="http://www.w3.org/1998/Math/MathML">
I haven't done much with books containing MathML but I've seen that structure in a couple of them.
The attached file seems to display happily in Sigil but not in calibre's ebook-editor.