You will need to edit the pages that contain the flash objects and add the following code between the embed and object tags:

Add the following code after the Object tag:

<param name="WMode" value="transparent"></param> 

And add the following code in the Embed tag:

wmode="transparent" 

It should look something like this:

<object width="300" height="220"> <param name="WMode" value="transparent"></param> <param name="movie" value="http://www.flash.com"></param><param name="allowFullScreen" value="true"></param> <param name="allowscriptaccess" value="always"></param> <embed wmode="transparent" src="http://www.flash.com" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="300" height="220"></embed> </object>