Unfortunately you cannot bypass the Save PDF File window from doPDF when printing.
Please follow u on this article on how to do a clean reinstallation of doPDF on your computer.
We tested the situation and doPDF prints in whatever order it receives from the source application (the default Windows Scanner and Fax). It does not alter the image order. You have to check if the order is not changed by the XP Scanned images viewer in the Printing options.