eStore doesn't use iframe so that won't be an issue.
Please setup the PayPal PDT following this documentation and it should fix this issue that you are having:
http://www.tipsandtricks-hq.com/ecommerce/wp-estore-instant-digital-product-delivery-499
I just entered some test value in the following eStore settings field to trick the plugin into thinking that you are using PDT:
WP eStore Settings -> Payment Gateway Settings -> PayPal Settings -> PDT Identity Token
When you use PDT, it doesn't clear the cart on checkout submission. For some reason, the cart clearing is messing IE up on your server but the above trick should fix that.
I tested it in IE and its working fine now.
Please check it out yourself and let me know how you go.