I think it’s the same situation on my setup. Yesterday evening I loaded the snapshot with it’s five layers after I removed all layers. Then the layer three has no audio output. The midi symbol on UI singnals that there is incoming midi but you don’t hear anything from layer 3. Maybe there are some issues on saving and loading snapshots when Zynthian is in multi timbral mode.
Is there a possibility to trace midi and audio routing in action during playing so that we can see where it gets interrupted? Or is the 2nd FluidSynth instance a reason?