Check that the Editor Profile Parameters allow IFrames

In the JCE Control Panel, click on the Editor Profiles button.

Click on the Profile name that the user, usergroup or component is assigned to, eg: Default

Click on the Plugin Parameters tab, then on the Media Support tab.

Check that the Allow IFrames is set to Yes to allow any content to be loaded in an iframe, Local Content Only to only allow content from the site, or Local Content and Supported Media Only to allow content from the site and content from Youtube, Vimeo, Dailymotion, Scribd, Soundcloud, Slideshare, Spotify, Facebook, Twitch, Ted and Instagram.

Allow iframes options

Configure Joomla! Article filters

By default Joomla!  cleans content on saving, removing script tags, event attributes (such as onclick, onmouseover etc.) and style tags.

A simple article parameter change is all that is required to fix this.

  1. In the Joomla Admin menu, go to System -> Global Configuration, click on the Text Filters tab.
  2. For the Super Users group, or any other trusted user group, set Filter Type to No FilteringMake sure that you only set this option for user groups that can be trusted as setting the Filter Type to No Filtering will essentially allow the user to include any html in an article. 

Alternatively, set the Filter Type to Custom Blacklist, and add an edited list of the default Blacklist tags to the Filter Tags field, with iframe removed, eg:

applet,body,bgsound,base,basefont,canvas,embed,frame,frameset,head,html,id,ilayer,layer,link,meta,name,object,style,script,title,xml

RSFirewall scambles tags

If you have RSFirewall installed, please read this article - http://www.rsjoomla.com/support/documentation/view-article/785-scrambled-tags-iframe-becomes-i-frame.html