If you are getting the Notification Emails but your customers are not getting their Confirmation Emails the most likely reason is that you have removed the pre-defined "email address" field from ShopFactory and replaced it with your own field.
Email Address and Country should not be removed from Customer Details.
Email Address is used to send the confirmation email to your customers
Country is used for Taxes and Shipping.
Do the following to restore the Email Address Field:-
Select Properties => Customer Details from the Menu and the following window will display
If the box next to Email is not Ticked, that means you have disabled the default email field, this is mandatory and cannot be removed.
Click on the box next to email to enable it. A window will popup - you can enter instructions there if you like, but I suggest you leave it blank. Just click the Ok button to close the window.
Now click on the Next button
This will now show the Delivery address fields, just click the Finish Button.
Now you can place a test order and you will see the Confirmation email is sent.
If you have removed Country you will need to do the same for the Country Field.