First test had a space it seems, so never matched

So something like: (second part not needed I guess, test might better)
 <xsl:choose>
    <xsl:when test="cac:TaxTotal[child::cbc:Amount][1]/cbc:Amount &gt;= 0">
     <xsl:value-of
select="format-number(floor(cac:TaxTotal[child::cbc:Amount][1]/cbc:Amount),'+0000000000000;-0000000000000')
"/>
    </xsl:when>

    <xsl:when test="cac:TaxTotal[child::cbc:Amount][1]/cbc:Amount &lt; 0">
     <xsl:value-of
select="format-number(floor(cac:TaxTotal[child::cbc:Amount][1]/cbc:Amount),'+0000000000000;-0000000000000')
"/>
    </xsl:when>

  <xsl:otherwise>00000000000000</xsl:otherwise>
</xsl:choose>