I’m seeing the same thing, I’ve manually updated to v2.9.1 and running WordPress v4.0 on GoDaddy windows hosting.

All plugins disabled, alternative themes work just fine.

Note that it isn’t just the theme interaction that is broken the widget screen loses all click and drag related events.

Here is the error from Chrome v37.0.2062.124 m developer console.

Uncaught Error: Syntax error, unrecognized expression: a[rel=] load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2fb.error load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2fb.tokenize load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2fb.compile load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2fb.select load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2fb load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2fb.matches load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2m.filter load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2w load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2m.fn.extend.filter load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2initLayout avia_colorpicker.js?ver=4.0:948(anonymous function) avia_colorpicker.js?ver=4.0:652m.extend.each load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2window.EYE.init avia_colorpicker.js?ver=4.0:651j load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2k.fireWith load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2m.extend.ready load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2J load-scripts.php?c=1&load%5B%5D=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.0:2