Hi Christoph,
You can use VI Server on the real-time target to launch other VIs dynamically. Your startup executable could be a simple application that uses VI Server to start other VIs that run in parallel in a pre-defined sequence.
Here's an example that does something similiar.
Note that when you build the VI into an application, you must include all the VIs that are called by VI Server as dynamic VIs in the application builder.
-Gerardo