Is Custom Google Search running the deprecated search API?

I have been getting this message for the last couple months, which is why I changed my custom google search plugin to WPMU's, but I'm still getting the message:

"This page is calling an old version of the Custom Search API, which is deprecated and will stop working soon. In order to avoid an outage for the search results, the call for search results must be updated to the current version of the Custom Search API https://developers.google.com/custom-search/docs/element."

I'm not sure if this is due to some old code in our header, or due to the plugin.