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Here's the first few lines from one of my epubs:
<?xml version="1.0" encoding="UTF-8" standalone="no" ?>
<!DOCTYPE ncx PUBLIC "-//NISO//DTD ncx 2005-1//EN"
"http://www.daisy.org/z3986/2005/ncx-2005-1.dtd">
<ncx xmlns="http://www.daisy.org/z3986/2005/ncx/" version="2005-1">
Perhaps you have standalone="yes" in your first line?
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