Now heres the strange bit. If I publish the main.fla as a .swf and play it in the standalone player - everything works (You can test this by downloading the bios.swf here and clicking on the bios button)
However if I publish the main.fla as a .swf and display it in a html page the menu system stops working.
I have no idea why this is happening and its immensly frustrating so if anyone can help it would be great.