HTML5 Video controls won't display if video not on Base Layer

This is my take on granting a user control of a video once they've watched it all the way through.

I have a video on the base layer of a slide which has video controls turned off.

I have the same video on a new layer where the video controls have been enabled.

I have custom javascript that tracks completion of the video, so the next time the slide is loaded the user is kicked over to the new slide layer with a trigger and everything on the base layer is hidden.

This works great in the Flash output, but there is a problem with the HTML5.  The HTML5 controls will not appear when you mouse over or click the video. It is almost as if something is covering the video, preventing the cursor from touching it.  I know the controls are there because I see them when the video starts, and then they fade away.

What could be preventing me from accessing the video controls via HTML5?