After upgrading from K 8.0 to 8.2 the check box inlude jquery in the javascript webpart disappeared and scripts are not working.
I think from 8.1 and more, you will have to declare your own reference to JQuery, to avoid confilcts. Take a look here
http://devnet.kentico.com/articles/using-a-custom-jquery-when-developing-pages-in-kentico
Please, sign in to be able to submit a new answer.