I'm not sure why this support thread was closed: http://wordpress.org/support/topic/eshop-cart-widget-not-automatically-updating?replies=21
I had the same problem today after upgrading wordpress from version 3.6 to 3.6.1 and eShop from 6.3.10 to 6.3.11.
@vincesta - you're solution worked for me.
Go to wp-content/uploads/eshop_files
You will find a file called eshop-cart.js
In this file replace all occurances of insertAfter() with after()
@esmi - There's a good chance that there's a plugin conflict going on, but with several people having the same problem, if simply changing the insertAfter to after fixes the problem rather than track down what plugin we might all have in common - isn't it worth looking into?