You can turn off the adds in your User CP. And you have to, it is not automatic.
You can also select to ignore or subcribe to threads in your User CP.
The User CP tab is located in the top left corner of the board. Users can use this to customize there options, information, and forum view. There are many options listed in the User CP to set up your account better to your liking.
Note: "remove these adds" does NOT remove the top banner add. Just all the rest.
When doing any upgrade it is best to clear out your cache's so previous information saved does not interfer with the new information added or edited.