this is covered in the FAQ Section of the Menu Writer support page:
Q: How can I get my menu to display over my Flash (.swf) movie?
A: In order to ensure that your Flash movie does not display over all other elements on the page, you need to apply the wmode="transparent" parameter to the <embed> reference for the swf file.
e.g.: <embed src="myflashmovie.swf" wmode="transparent">
View the following link for more information: tn_15523.html