You say therye not showing up in the ProPDF folder, but is it creating the pdf at all....will it display on screen as a PDF if you check this box? If it will display the PDF, then it must be saving it somewhere. If it wont display it, then you have a different issue than it just not saving to the correct folder.
I have a similar problem. Proseries tells me it created the file successfully in the dialog box that appears after printing, but it does not display the pdf when the box is checked to do so, and it does not appear in the folder I have defined in the print center. Any idea why this is happening? Thanks.