Hi Karin,
We'll need to take a look at your files in order to see where the problem is coming from. Could you please log a support case at
http://na.justsystems.com/contact-support.php? To help us investigate more quickly, could you also please send me a copy of the PDF file that looks wrong, and a copy of a PDF file that looks the way you want it to look? Also if you could zip up and send me the files that you have customized in your XMetaL installation, that would be useful as well. I'm at syeo at justsystems dotcom .