Update:
Comments below are informative, from the comments: The solution was to remove the jQuery reference in the master page and let the Brava solution take over. Although this did seem to cause some other errors.

Original:
The JQuery in the custom master page can easily be modifying anything on the html page including the standard SharePoint context menus.

JQuery generally works by selecting an object or objects first that a function will then be applied to.

    $('#id_of_some_html_element').somejqueryfunction(some parameters...)

from the first error I would say whatever $('#id_of_some_html_element') is selecting it does not have the .hoverIntent function/method or property... or maybe the selection $('#id_of_some_html_element') is not actually finding the object on the screen at all.

With that said I think JQuery has a .hover but not a .hoverIntent I do not know if skel.js provides the plug in for hoverIntent or not. But googling for a JQuery plugin with hoverIntent does find this http://cherne.net/brian/resources/jquery.hoverIntent.html 

if your site is really using that one or not I do not know.

I would first check the custom master page and make sure the js include paths are correct and the js files exist. I would open up the skel.js files and verify to make sure hoverIntent is not defined in them skel.js if not I would add the hoverIntent plugin for JQuery in the master page and try that.

With that said I think OpenCalloutAndSelectItem is part of SharePoint javascript API and if that's undefined... Then I would first check the custom master page for a small typo that is stopping the other javascript files from being included - a missing closing tag on a script tag, or something like that.