Bear in mind the iframe method is only necessary if you need to redirect buyers to a page on your own site after checkout, instead of using the standard thank-you/download page that E-junkie normally generates for you.
Regardless, that should not affect PDF Stamping, as the actual download link is the same either way. Make sure you're placing actual test orders through a checkout (even if only our Free Checkout for a 0.00 order total), rather than using "Send free download link" which would not engage the stamper. Also, after you upload a .pdf file for a product that you want to be stamped, make sure you wait at least 15 minutes before testing the stamping feature for that file.
If the above does not explain your issue, please email our Support team a copy of your PDF file, and copy the Payment Variable Information URL setting you're using and paste that into your email as well: