so it sounds like you are using PayPal Payments pro?
And when the customer fills in the CC details on your site it works? I want to clarify this because it is possible to use CC details when going through Express checkout to.
payPal Payments Pro offers 2 services:
1) direct payments: this is when the customer fills in CC details on your site and sends the transaction to paypal
2) Express Checkout: This is when the user is directed to Paypal, on Paypal's site they can pay using the PP account, or they can select to not use a paypal account and enter CC details
When using Direct pay,tents, it goes through the Confirm page then to the checkout success page.
When using Express Checkout, it goes through the pp_confirm.php page, then to the pp_chckout_success.php page.
that could explain the emails not sending if the email settings on the pp_ pages being different from the Direct checkout pages. If you would like me to double check, please provide a link and ftp info in the private message section.