The PDF Writer has a hardware margin of 0 (zero). This enables the installed printer to write to the edge of the paper. Normally this is a great feature but sometimes it may be a problem because the created PDF files are sent directly to a physical printer without scaling it to fit the margins of the physical printer.
Creating a new Form
In case you want to use a hardware margin together with the PDF Writer, you have to create a new form (paper size) on your system. New forms are easily created from the Control Panel list of printers. Just open the File menu and select Server Properties.
From the list of available forms you should select the one that you want to add margins to. In this example we will choose the A4 form.
Click the Create new form checkbox to design a new form. Enter a name and changes the margins. Select Save Form when you are done.
When the new form is saved, you should go to printer properties of the PDF Writer. Here you click Printing Preferences. In the next dialog you click Advanced. Now you can select your new form as the default paper size of the PDF Writer.
That should do the trick.