If the only problem is Acrobat prompting for a filename, you can stop that by changing a setting in the Acrobat print driver.
1) In Windows, go to Start->Control Panel->Printers and Faxes
2) Right-click the Acrobat Distiller, and select Printing Preferences
3) On the Adobe PDF Settings tab, set Adobe PDF Output Folder to the desired output folder. The important thing is to *not* have it set to "Prompt for Adobe PDF Filename"
4) Click OK
Now your batch procedure should work. Note that Acrobat may generate random names for your PDF files in this case (derived from the random names Arbortext assigns to the temporary postscript files). If that's a problem, you can try poking around in packages/tools/pub_*.acl, where you can probably find a function that will let you specify the final PDF filename when you print. (We use a system like this, but we use XSL-FO instead of FOSI, so I don't know if you'd be able to use exactly the same function we use. FWIW, the function we use is _pubpdf::publish_pdffile().)