Still getting Flash after Storyline upgrade in my Engage Document.

So I have several StoryLine projects which include Engage documents.  I upgraded to StoryLine 3 to remove the Flash and after zipping and launching in Axonify I still have Flash in the Engage docs.  I am choosing HTML 5 only in the publishing window.  If I publish/ Zip and load the Engage file directly to Axonify, I don't have the issue.  What the Flash is going on with the Storyline?   

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