Hi Andrew,
The export from Artisteer contsains only part of what you need for a mojoPortal skin. If you did not start with an existing skin then your skin is missing needed files therefore it doesn't work at all.
The most important step is choosing the correct skin to use as the starting point from the table in the article Creating Skins from Artisteer Html Exports. Read that article very carefully and it should get you on track. The main difference in the skins in the table are the variations in layout.master file needed for various layouts that can be produced in Artisteer. If you chooose the wrong one the layout will not be correct. The table tells you how to choose based on settings in Artisteer for header footer and menu. If you choose incorrectly the layout won't be correct but if all else fails you can try copying the layout.master file form each of the skins mentioned in the table into your skin folder until you find the correct one.
Make sure you are using the latest verison of mojoPortal 2.3.8.1 and using Artisteer 3.1
Hope that helps,
Joe