aki128

I found a solution for this. There’s a Z-Index value in the plugin Element properties which is set to 1 by default. However, Twenty Eleven theme uses its own Z-Index value 9999 for the header image, so it’s needed to change this in the custom CSS.

Go to the Appearance -> Customize and click on Additionnal CSS option. Then insert this line:

#branding {
	z-index: 1;
}

And click Publish. The animations from the WordPress Animator should be in the foreground of the header image now.