The ASP.NET worker process probably does not have the privileges to modify the user.config file in your portal installation folder. MonoX user manual says:

By default, when ASP.NET allows anonymous access, the application runs in the context of a
special local account (this is NOT a domain account). In Windows 2000 and Windows XP, ASP.NET applications run under the account called ASPNET. In Windows Server 2003, the account is called NETWORK SERVICE. These user accounts are created during the .NET Framework installation process with a unique, strong password, and are granted only limited permissions.
MonoX installation wizard will try to set the write privileges on the folders that require it (/RssStorage, /Logs, /Cache). This process may fail due to your local security configuration; please make sure that the ASP.NET machine account has full write access on these folders (right click on a folder using Windows Explorer, Properties, Security).

You can also change the following key in the user.config file to achieve the same effect:

<add key="InstallationDone" value="true" />

The value should always be set to "true" when the installation is finished.