Yesterday I came across a right little pain in the butt! I found that swf objects display on top of all layers regardless of z-index.
I found the solution was to add this line in the markup.
<object type="application/x-shockwave-flash" data="/someMovie.swf" width="100" height="100">
<param name="movie" value="/someMovie.swf" />
<param name="wmode" value="transparent">
Problem is this doesn't work in firefox, does anyone have a cross browser solution to this???