I tried your skin on my machine and it does not have the problem that I see on your site, it works correctly here. Are you using .NET 4 or .NET 3.5 medium trust?
There can be problems under .NET 3.5 medium trust as discussed on the bottom of tha rticle Understanding the theme.skin file
On your broken site if you view the source of the page you will se that the menu markup is not correct for Artisteer, if you compare it to the working site you will see what it should render as. This is controlled by the theme.skin file.
You may need to copy the theme.skin file from the skin folder into /App_Themes/Default and you will not be able to use more than one skin in the installation if they require different theme.skin settings.
Under .NET 4 there should not be any problem, this problem should only happen under .NET 3.5 with medium trust.
Hope that helps,