This was reported before, but not resolved, or explained.
I am on version 1.7.08 (which is currently latest).
The option “Optimize cut path” is OFF.
The layer which is last in the setup order is being cut first (this one is outermost shape) then the order seems in order, but makes a lot of trouble because it is first cut out of the plywood board and then the shape bends and the laser then engraves on the bent plywood - I have a reason for cutting last.
I am convinced that if you do not specify (in the “Optimize Cut Path” window) that you want the project to be cut in layer order the controller will not respect that wish.
It will probably generate a path according to another logic that one of the programmers will be able to clarify.
This usually means, “I have no idea if the mouse accidentaly selected something I did not know about.” If it was a bug in the software, there would be a lot of people reporting this.
V1.7.08 is a long ways from v1.2.03 you used as an example.