I suspect that the content on top of your stamp is actually an annotation (and is not part of the page content stream).
In PDF document annotations always ‘float’ on top of the page content.
In your case you are using ‘pdftron.PDF.Stamper’ to add new content to an existing page. The content is added to the content stream but there may be annotations that could obscure any content.
As a workaround you could
a) remove or flatten all annotations (e.g. doc.FlattenAnnotations(false)) prior to stamping
b) add your stamp as annotations. You can do this with stamper.SetAsAnnotation(true).