Ahh.. I see where the confusion is coming from. Deleting the user from Joomla doesn't revoke the application approval in Facebook. Therefore, if you use that same user again, they'll just need to enter their credentials but the permissions will be skipped (they already granted approval for your Facebook application).
If you want to see the permissions dialog again, you'll need to delete the approval for that application from your user's Facebook account:
- In Facebook, click Account Settings -> Privacy Settings
- In the bottom left of this page, hit "Edit Your Settings" under "Apps and Websites"
- In there, you can delete the approval given to any application.
Once done, you'll get the permissions pop-up when you return to the site and try to login or register through JFBConnect.
Hope that helps you test, and good luck!