The warning prompt mechanism is broken.
I updated my September Jessie Pixel install as indicated in the blog,
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sudo apt-get update
sudo apt-get dist-upgrade
sudo apt-get install -y pprompt
and upon reboot I got the warning, but the default "pi" user password has most definitely been changed. To confirm it I opened a terminal and tried su - pi, and after entering raspberry it gave me an authentication failure. I also restarted and tried logging into pi/raspberry and was told I had an incorrect password, so something is definitely wrong with the code that checks to see if the prompt needs to be displayed.
I am not logged in as "pi" because I created my own user account. The "pi" user account was secured by setting a long random password, then locked (sudo passwd -l pi), but every time I restart I get the warning.
EDIT: Even after removing ppromt and rebooting I still get the warning when I log in as my user via SSH.
While I can appreciate why you did this, and fully agree that Raspbian needs to be more secure, it seems it needs a bit more testing.
I'm guessing the problem is due to me changing the pi account password from my own user account. So now I'll have to undo everything I already did to secure the pi account in the first place just so I can login as pi and re-secure it.
My password is the last 8 digits of Pi.