Hi Adam,
it is definitly not correct to have multiple XMP sections in one PDF file.
This seems to be a but on on or the other side, but to address this we would need more info.
You can either post an example of such a wrong PDF or you inspect the files and try to find out, which tool and version created these,
here is an example:
<?xpacket begin="" id="W5M0MpCehiHzreSzNTczkc9d"?>
<x:xmpmeta xmlns:x="adobe:ns:meta/" x:xmptk="Adobe XMP Core 4.1-c036 46.275676, Tue Feb 13 2007 11:19:12 ">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about=""
xmlns:xmp="http://ns.adobe.com/xap/1.0/">
<xmp:CreatorTool>Adobe Illustrator CS3</xmp:CreatorTool>
...
Thanks,
Stefan