I think I have have now a little idea what’s going on there:
In my setup I have 2 instances of Fluid Synth, one instance should be on layer 3 and the other one on layer 5. But when you take a look into the running setup (VNC engines, patchage) there you see that there exists only 1 FluidSynth engine! And the corresponding midi event filters are setup in the wrong way. Normally there should be one midi_event_filter per layer. And midi_event_filter_02 and midi_event_filter_04 should be connected to each their own FluidSynth instance.
When I was entering the configuration into Zynthian the first time, everything was running fine. After storing the Snapshot, shutting down Zynthian and restarting Zynthian my setup was confused.
Any ideas how to solve this? Are there some limits handling multiple engine instances?