Hi Danny,
The problem is that you should not "publish". mojoPortal is a web application project type not a web site project, the packages on codeplex are already compiled and ready for deployment, they have no C# source code, re-publishing them messes it up.
When you open the deployment files in WebMatrix or VS its treating it like a web site project rather than a web app which is what the actual source code is. And when you publish it is further compiling it into a pre-compiled web site. The problem with that is that VirtualPathProviders do not work in pre-compiled web sites, therefore the VirtualPathProvider we use to map the the theme.skin file from the skin folder does not work and therefore skins don't work.
There is a kind of hacky way to solve that problem as discussed on this thread but, the hacky solution won't work in medium trust hosting which most hosts use.
To work with mojoPortal in Visual Studio it is best to get the source code rather than try to use the already compiled deployment packages for development.
Hope that helps,
Joe