I have both Nuance's PDF Converter Professional and Adobe's Acrobat Reader on my system.
When I open up a PDF I want it to open up in Nuance's PDF Converter Professional. But when I view a PDF in the Viewer Pane I want it to be viewed in Acrobat Reader, as Nuance's product doesn't work in the viewer pane.
Do you see the same problem if you view a PDF file in IE?
Reinstalling Adobe Reader will probably make it the registered ActiveX handler for PDF files, which should solve the problem. (Whichever of the two programs was installed last should 'win', and you can then modify the PDF filetype to decide what happens when the files are double-clicked.)