What is the exact text of the "file permission error"? If it's the message that I suspect, this message really means that FileMaker was unable to create a PDF, it then suggests several possible causes--one of which would be a permission issue, but the most common cause of this error is an invalid file path or file name.
My guess is that if this is a script that is saving your PDF's, that the filepath specified in your script needs to be updated to be a valid filepath on your new computer.
Try this test before replying with the exact text of your error message: Go to any layout and use Save As PDF from the File menu to save a file to your desktop. If that works, then several possible issues with FileMaker and Adobe can be ruled out.