Interesting. It looks like the new ACF (Advanced Content Filtering) in CKEditor 4.1 strips out the iframe tags. There are a couple of ways to work around/with ACF according the docs:
It seems like a bug with 4.1
Ok, I've added the following line to the CKEditor config and it seems to be working as it did before.
'extraAllowedContent' => 'iframe[align,frameborder,height,longdesc,marginheight,marginwidth,name,sandbox,scrolling,seamless,src,srcdoc,width]; *[accesskey,contenteditable,contextmenu,dir,draggable,dropzone,hidden,id,lang,spellcheck,style,tabindex,title,translate](*)',
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