I did some more investigations. I updated both StartupApp.exe and MonoBrickFirmware.dll in /usr/local/bin. Afterwards I rebooted and EV3 booted correctly. However, when I tried to start my application I still got the same error. Then I created a new Console Project within the MonoBrick solution and put all my stuff into that. And now it works. But I still do not know why it doesn’t work with the projects that lives in it’s own solution.