Hello -
When we add an item to the cart, we are still seeing the pop-up add-to-cart.
When we go through the process and view the cart, then we see a page that looks normal for VM.
What are you expecting it to do? If you want to make changes in how the shopping cart page looks, then those have to be done under the FlyTabs theme. We provide a copy of the standard shopping cart page in our VM theme where you make changes.