If I get an HTML email and try printing it, doPDF is grayed out within the printer drop down. When I click print, it prints to my default printer. Non HTML emails give me the option what printer to use.
We tried to troubleshoot your issue but the HTML mails were successfully converted to PDF files and we could choose doPDF from the printers list. We tried both Outlook 2007 and Mozilla Thunderbird on our tests.
Please try to either reinstall doPDF and use the latest version and built for it and also try with other mail clients as well as the ones i mentioned perhaps it is a mail client issue or restriction.