Hi Andy,
What happened is that in Artisteer 3 they now have more variation in the outer markup and we don't currently have included skins with each possible variation so in some cases it requires moving things around in the layout.master file. You can see the difference when you view the source of the exported page and compare it to viewing the source of your site. In the exported html the heading and nav are outside of the sheet whereas in your layout.master they are inside the sheet. So you just need to compare that outer skeleton of markup from the html file and adjust the skeleton markup in your layout.master to more closely match it.
At some point I'd like to figure out all of the possible variations and try to add more starter skins that match them, but even then part of the problem would be figuring out which one to use would still require looking at the exported markup.
Hope that helps,
Joe