The only other thing i could think of that could manipulate an element beyond JS is a stylesheet, so i then went about blocking stylesheets one at a time and narrowed it down to being something inside the main stylesheet for the theme, ie. this one.
I don't know specifically which style or styles in there are causing the issue, but my suggestion would be to go through the stylesheet and delete chunks of CSS at a time, then refresh the page to see if the problem is still there, if it is, keep deleting more chunks until you find the area of CSS that causes the problem.
You only need delete CSS temporarily, just to narrow down specifically which area of theme's styling is at fault, but blocking that stylesheet did get rid of the double fade(which tells me it's definately that file causing the problem)
Hope that helps. :)