In project explorer, create build specification under the target and create the .exe. Right click on the new build specification and select ' Set as startup'. You will notice a small change in the appearance of the icon in the project explorer. Now you can right click the build spec and deploy it as a startup app.
many thanks for the hint. It seems to work, because I recieve the following message after software reboot and re-connect to the target: This VI is part of a Real-Time Startup Application. All VIs on the target will be closed if you choose to refresh and continue with deployment.
It would be better, if the start-up VI's keep on running. But it is not a problem, because I can then start them manually.
At the moment I can't test a hardware reboot, because the system is installed on an other location.