youtubenopause.userscript.js

// ==UserScript==
// @name         Video was paused killer
// @namespace    http://tampermonkey.net/
// @version      0.1
// @description  Kills the "Video paused. Continue?" box that pops up every once in awhile
// @author       Nett18 - github.com/kres0345
// @match        https://www.youtube.com/watch?v=*
// @grant        none
// ==/UserScript==

(function() {
    'use strict';

    window.setInterval(function(){
        if(document.getElementById("main") != undefined){
            document.getElementsByClassName("style-scope yt-button-renderer style-blue-text size-default")[0].click();
            document.getElementById("main").parentNode.removeChild(document.getElementById("main"));
        }
    }, 5000);
})();

Please note: I haven't tested the finished script since I did not get any more boxes.