It may have more to do with the client's Preferences than anything you are doing.
Take a PDF and open it in Acrobat and go to File | Properties | Initial View and see what the magnification is set to. If it's set to default, try changing it to Fit Width or Fit Page and then save the PDF and reupload it.
The other option is you can use try embedding the PDF using javascript (
http://pdfobject.com/). That script gives you the ability to set a magnification for each document.
