As others here have posted, after the new version is installed, eShop seems unable to handle PayPal transactions and gives with the message "The transaction was not completed successfully. eShop could not validate the order." when transaction emails are sent out.
I just upgraded both the plugin to the newest version as well as upgrading WP to version 3.4.1. After over a year with no issues with eShop, when I went to do a test transaction, I received the "The transaction was not completed successfully. eShop could not validate the order." email after completing it.
So, I went to forum and checked out the PayPal Setup Page at http://quirm.net/wiki/eshop/setting-up-merchant-gateways/paypal/. IPN was set to OFF, as directed on the Setup page. Shipping was being handled solely by eShop. Some of the other information on the Setup page is outdated, as when you click on the "Encrypted payment settings" section, you are only given an option add, edit or remove a certificate. There is no option there to turn "Auto Return" to OFF there. So, that page needs to be updated to reflect the recent PayPal page layout updates.
Anyway, after putzing around for a little while, seeing if my setup was incorrect in any way (even though it had not been changed in any way since I setup eShop last year, nor had I made any changes to my PayPal setup) and having no luck, I decided to just revert the plugin back to version I have been using since last year, version 6.0.2.
Viola! The test transaction went through just fine and both PayPal and eShop marked the transaction as completed instead of pending.
Considering how many people have mentioned this error since the new eShop version came out, especially those like me, who have used earlier versions without a hitch, it seems to me that the updated version of the plugin is flawed in some way. Or maybe PayPal changed something on their backend with the new layout they rolled out recently that is causing issues between itself and eShop.
For now, I recommend using version 6.0.2, as it appears to be working just fine with PayPal.