<xsl:template match="/">
That matches the root of the document, not the element that you have
confusingly called Root (which is its child) so
<xsl:apply-templates/>
applies to <Root> which recursively applies the default template to all
elements of the docuemnt.
<xsl:template match="/">
<Root>
<xsl:apply-templates select="Root/Header"/>
</Root>
</xsl:template>
would work, or simply
<xsl:template match="/">
<Root>
<xsl:copy-of select="Root/Header"/>
</Root>
</xsl:template>
David
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