The problem seems worse then that: not all project types I previously had show up in the “New project” wizard.
There is something wrong with the latest GHI installer. I already uninstalled everything from GHI and Microsoft .NET Micro Framework 4.2 QFE2 SDK and reinstalled everything, still the same.
We recently split the package up into two parts, the 4.2 package and the Optional 4.1 package. The templates that you are looking for in your second post are in the 4.1 package right below the “main package”. It is possible that the firmware updater you are using is trying to find the 4.1 directory that doesn’t currently exist on your machine. Try installing the second package, and let us know if you still have the problem.