PayPal have changed the behavior of how the payment data gets posted back to your site slightly. More details here:
http://www.tipsandtricks-hq.com/forum/topic/paypal-enhanced-checkout-issue
I have added a new feature in eStore that uses PayPal's PDF feature to display the download links on the "Thank You" page which is a more robust way of doing this. The documentation has been updated accordingly:
http://www.tipsandtricks-hq.com/ecommerce/wp-estore-instant-digital-product-delivery-499
Bottom line.... all of your stuff is working fine as I understand. You just need to use this new PDT option in eStore and then your download links will start to show up in the "Thank You" page too.
If you need an update for the eStore plugin then this link should help:
http://www.tipsandtricks-hq.com/forum/topic/how-and-when-do-you-get-an-update