I suspect that your site is not configured for the correct version of ASP.NET, possibly it is configured for 1.1 .NET. mojoPortal requires .NET 3.5 SP1, but in IIS it will not list it as version 3.5 but version 2.0 because really 3.5 is a superset of 2.0.
Note also that if you have .NET 1.1 apps running on the same machine, you must use a different application pool for 2.0/3.5 apps, you cannot have both 1.1 apps and 2.0 apps using the same application pool. You would create a new application pool and use it for the 2.0/3.5 apps.
Hope it helps,