Hopefully, Xara developers would like to confirm
if this error is reproducible in the PDF export
in version 6.

Notice that when I opened the pdf file exported
with layers (using contoned images) in Illustrator,
the program reported an error about an "Unreleased"
format and individual images appears deeply nested
inside groups that I do not created.

So, the key points to investigate are:

Contoned grayscale images with Stained Glass
transparency on different layers, exported
as PDF with layers.

Alejandro