I also received this message just now, while I was testing my checkout pipeline and placing an actual order with a credit card.
The last few days, I generated a discount code and used that to test free checkouts. That process worked perfectly, and the PDFs were stamped correctly.
Today, I used a discount code that resulted in a $0.95 price, and I checked out using PayPal (without signing in to my PayPal account). The order went through and the PDF was delivered, but it was not stamped. I then received the "Server not notified for..." email.
Seems like there's something wrong on e-junkie's end today? Has anyone else seen PDF-stamping problems with regards to paid orders?