These things are controlled by the theme.skin file. The problem under .NET 3.5 medium trust is that VirtualPathProviders do not work, so instead of using the theme.skin file from the skin folder, all skins use the one from /App_Themes/default. So you can solve it by copying the theme.skin file from one of your skins into the /App_Themes/default folder replacing the one that is already there. As long as all your skins are from the same version of Artisteer it should work fine. Artisteer 2.3 used mixed case class names whereas in Artisteer 2.4 they changed to all lower case.
Note that under .NET 4 VirtualPathProvider does work in medium trust.
Hope it helps,
Joe