Z-index not working when Flash file is used

Z-index usually do not work when you have a flash file embedded, for this you have to set wmode to transparent

Following are the two main things that need to be changed or added

<param name=”wmode” value=”transparent”>
and
wmode=”transparent” inside the etc. tag.

wmode is an optional parameter in Internet Explorer 4.0 and higher, that allows you to take advantage of the layering, absolute positioning, and transparent movie features. When you add the parameter tag for wmode and edit it into your embed src tag (it must be in both), it lets you set all non-object areas of the Flash movie to transparent, opaque, or window. The later creates a separate rectangular window.

Reference:-

http://animation.about.com/od/flashanimationtutorials/ss/flashwmode_4.htm