Fancybox
After upgrading from 3.0.x to 3.1.1 I'm getting Fancybox conflicts that prevent it from working with Tubepress, it was working in 3.0.x. My theme is loading fancybox.js via the wp_enqueue_script function so that it isn't duplicated when your plugin or other plugins attempt to reload it. You appear to be loading it again within your inline JS rather than the WP enqueue function? It is conflicting with the previously loaded one. How do I change the settings to prevent this conflict so that Tubepress doesn't call this script a 2nd time?
Tinybox
I attempted instead to use the Tinybox playback method and the popup video box worked but the Tinybox stylesheet (vendor/tinybox/style.css also loaded with js rather than wp_enqueue_style) has styles applied to the body and h1 tags among other generic html tags that are causing display issues on my site.
Shadowbox
My 3rd attempt, this time with Shadowbox, proved unsuccessful as well. The browser console is showing that the Shadowbox script path is incorrectly called at http://mydomain.com/...ib/shadowbox.js when the correct path is http://mydomain.com/wp-content/plugins/tubepress_pro_3_1_1/src/main/web/players/shadowbox/shadowbox.js (no 'lib' directory)
Also, it appears that you don't use the wp_enqueue_script for anything other than jquery and tubepress. Just curious why you don't use the wp_enqueue_script and wp_enqueue_style methods to load all the other styles and scripts to prevent conflicts with other plugins/themes and allow for easy dequeueing if necessary?