Never had this problem until recently. When right-clicking a pdf document within DT to choose the app to open it (PDFPenPro), it fails to open. The document will open if selected Preview as the app to open it, but no longer will DT allow me to choose PDFPenPro to open the document within DT. I now have to start up PDFPenPro and then navigate to the actual document in my Finder to open it. THis seems like a strange bug to me. Never had this trouble before.
I just checked. I right-clicked on a PDF document in the Three Panes view, chose ‘Open With’ from the contextual menu options, then chose PDFPenPro. The PDF opened as expected under PDFPenPro.
Does your problem persist after a restart of the computer?