iText 5.5.3 + XFAWorker: Repeated section not rendering - itext

Question

We are using iText Java 5.5.3 with XFAWorker to inject XML into PDF templates and flatten those to simple PDFs.
To integrate into a system that has parts built in various technologies we have wrapped it into a http-Server using the simple framework
The injection stage works fine, but after flattening some sections are lost.
Detailled information:
The PDF template we inject into is: CLAIM.Plan.pdf.
Sample data we try to inject is: plan_v4.xml.
Without flattening we get: CLAIM_plan_unflattened.pdf.
With flattening the result is CLAIM_plan_flattened.pdf.
plan_v4.xml has multiple instances of //form/PlanItems/PlanItem and [CLAIM_plan_v3.pdf][6] is repeating the section to display all of them. This is the OK case. [CLAIM_plan_v4.pdf][7] is not showing the repeated sections for the individual PlanItem instances. This is the broken case.
The main bit of code that uses iText looks like this:
// load the XML document that contains the contents of the data element.
// NOT the <data> element itself or anything else.
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
dbf.setNamespaceAware(true);
DocumentBuilder db = dbf.newDocumentBuilder();
Document newdoc = db.parse(new InputSource(new InputStreamReader(xfaStream, "UTF-8")));
Node newdata = newdoc.getDocumentElement();
// Open the PDF and extract the complete xfa.
PdfReader reader = new PdfReader(pdfStream);
XfaForm xfa = new XfaForm(reader);
Document doc = xfa.getDomDocument();
// Remove all contents of the <data> element
NodeList list = doc.getElementsByTagNameNS("http://www.xfa.org/schema/xfa-data/1.0/", "data");
Node child;
do {
child = list.item(0).getFirstChild();
if (child!=null) {
list.item(0).removeChild(child);
}
} while (child!=null);
// Replace <data> with the new xml to inject.
list.item(0).appendChild(doc.importNode(newdata,true));
ByteArrayOutputStream os = new ByteArrayOutputStream();
PdfStamper stamper = new PdfStamper(reader, os, '\0', false);
xfa.setDomDocument(doc);
xfa.setChanged(true);
XfaForm.setXfa(xfa, stamper.getReader(), stamper.getWriter());
stamper.close();
If I now just finish quickly:
response.getOutputStream().write(os.toByteArray());
I get the good (but unflattened) result.
If I add the flattening stage like this:
com.itextpdf.text.Document document = new com.itextpdf.text.Document();
PdfWriter writer = PdfWriter.getInstance(document, response.getOutputStream());
XFAFlattener xfaf = new XFAFlattener(document, writer);
xfaf.flatten(new PdfReader(os.toByteArray()));
document.close();
The result is flattened but missing the repeated sections.
Can someone tell me what I am doing wrong so the PlanItems don't get rendered in the final PDF?