The batch print tool relies on external PDF reader tools, e.g. Acrobat for the DDE method, and the default shell PDF reader (if it has a shell print verb configured), and is not working properly with new Acrobat/Windows versions for the DDE (Dynamic Data Exchange) server method (I need to investigate why and fix it, if possible).
Next version will include a builtin print solution, making this tool functionality independent of what the user system has available.
But the best approach to your problem may be the use of the
merge tool, menu Tools>Merge\RearrangePages, to merge all the documents you wanna print, in the required order, and then print the result PDF from your preferred PDF reader. Do you see any problems with this method?