Hi,
I would check the mojoPortal log for clues under Adminsitration > System log
If there is any mistake in your layout.master file that prevents it form loading it will load an alternate faillsafe master page to prevent from crashing the page and it will log an error. My guess is that is what is happening and the failsafe master page is not the same as yours so it doesn't have the addiitonal panels and some things are in different places.
You cannot use existing skins in Artisteer. Artisteer is a design tool, it doesn't know anything about mojoPortal or mojoPortal skins, especially ones that were not created in Artisteer to begin with. For the skins we ship that were created in Artisteer we also ship the .artx file in our ArtisteerFiles.zip download so you can open those in Artisteer and modify the design and re-export the css.
Hope that helps,
Joe