Like whitey said, you should use server based directives over client based, much easier to control. In nw admin, create a new Directive, name in to whatever you want. Then specify path where you want the directive to start, / is the root on both Windows and Unix. If you want to exclude all directories named PDF then use +skip instead of skip, as + traverses the filsystem. If you want to exclude just one PDF dir, then use that path between << >> instead of /. If it´s directories you want to exclude make sure you add all possible cases of the dir name, as "PDF" and "pdf" are not treated as the same name.
<< / >>
+skip: PDF pdf Pdf
If instead you want to skip all pdf FILES, you must use this:
<< / >>
+skip: *.pdf
Then just edit the client resources and select the new directive. Hope it helps!
Cheers!
Maverick