Hi Gudni,
I just tested it and it worked correctly for me. My steps were:
1. download and extract mojoportal-2-3-9-4-sqlce-net40-deploymentfiles.zip
2. copied the www root folder to a location on my hard drive where I want the site files
3. I renamed the wwwroot folder as sqlce2394matrix
4. I installed the latest WebMatrix 2 from the Platform Installer sinc eI did not have it installed
5. In windows explorer I right click the folder sqlce2394matrix and choose "Open as Web Site In WebMatrix"
6. When WebMartix opens I click in the upper left corner Run in Internet Eplorer
7. The setup page creates the database and runs the scripts and the site works after that
Hope that helps,
Joe