It's best to contact the vendor (Nuance) in cases like this because often it's related to a specific issue that a specific product has with a specific PDF.

Note: Adobe Reader and to a lesser extent Foxit Reader automatically repair malformed PDF files when they open them, so sometimes this masks issues that can then show up when you're performing other actions on the PDF files.

Check with Nuance to see if they can find any error in the PDF or if you have Acrobat you can use the Preflight tools to look for some issues yourself.