Hi Lee,
Rebooting the machine would clear server side cache but to my knowledge it would not clear the browser cache, that is persisted to disk.
If your menu is not in the correct place it maens you did not choose the correct starting skin based on the criteria in the left column of the table in the documentation. You need to look at the menu properties in Artisteer, is it inside the header, below the header inside the sheet or above the header inside the sheet or outside the sheet. These differences are all reflected in the variations of the layout.master file in the incldued Artisteer 3.1 skins, so you could try replacing your layotu.master one by one from each of the included skins until you fiond the right one, but best to choose based on te criteria.
Make sure you are editing the correct location, ie /Data/Sites/[SiteID]/skins/[skinname]
Easiest way to make sure css changes are loaded is to reset the skin guid under Administration > Advanced Tools > Design Tools > Cache Tool
Reseting the skin guid appends a new gud to the url of the skin css handler thus byapssing any previous browser cache.
Hope that helps,
Joe