I checked to see if this has been reported before. I didn’t see it, so here goes. If a bunch of pieces are placed in an at-start stack, it appears the software forces them to be in a Stack even though piece traits might deem them not stackable together. For example, in an at-start stack, I put an infantry unit (at board layer “ground”) with a fortress counter (board layer “bottom”). The fortress piece was supposed to be rendered beneath the infantry unit. However, the software placed the fortress on top (it was the last listed piece in the at-start stack) and kept them in a stack until I pulled them apart. This behavior caused anomalies. For instance, at one point the stack overview showed the single infantry piece twice with the fortress sandwiched in between. The s/w probably should either throw an exception or be more robust when decoding the units in an at-start stack.
Of course, I got around it by putting the units in different at-start stacks. However, I don’t know what happens if I put multiple unstackable units in an at-start stack. It caused me a bit of confusion as I tried to sort it all out, and it probably would cause real headaches for a less experienced user.