I don't know of any change in mojoPortal that could break something in the Ajaxtoolkit. Maybe the newer versions of jQuery and jQueryUI have a compatibility problem with it, you could try changing the version to an older one from Web.config if you're using the CDN.
Only other thing I can think of that is different is the combining of scripts, you could disable that by setting CombineScriptsWithScriptManager="false" on the <portal:ScriptLoader in your layout.master to see if that is a factor or not.
Hope that helps,
Joe