Lets try to pass in a value for shipping to the PayPal checkout page which should make it so that PayPal will not apply the profile based shipping for checkout from this site. Please open the “eStore_payment_submission.php” file and search for the following:
//$myPaypal->addField('shipping_1', $shipping);
$myPaypal->addField('handling_cart', $shipping);
once you find it change it to the following:
$myPaypal->addField('shipping_1', $shipping);
//$myPaypal->addField('handling_cart', $shipping);
Then try a checkout and let me know how you go.